def suffix(): #pylint: disable=unused-variable import os from mrtrix3 import app global _suffix if _suffix: return _suffix fsl_output_type = os.environ.get('FSLOUTPUTTYPE', '') if fsl_output_type == 'NIFTI': app.debug('NIFTI -> .nii') _suffix = '.nii' elif fsl_output_type == 'NIFTI_GZ': app.debug('NIFTI_GZ -> .nii.gz') _suffix = '.nii.gz' elif fsl_output_type == 'NIFTI_PAIR': app.debug('NIFTI_PAIR -> .img') _suffix = '.img' elif fsl_output_type == 'NIFTI_PAIR_GZ': app.error('MRtrix3 does not support compressed NIFTI pairs; please change FSLOUTPUTTYPE environment variable') elif fsl_output_type: app.warn('Unrecognised value for environment variable FSLOUTPUTTYPE (\"' + fsl_output_type + '\"): Expecting compressed NIfTIs, but FSL commands may fail') _suffix = '.nii.gz' else: app.warn('Environment variable FSLOUTPUTTYPE not set; FSL commands may fail, or script may fail to locate FSL command outputs') _suffix = '.nii.gz' return _suffix
def execute(): #pylint: disable=unused-variable if utils.is_windows(): raise MRtrixError('Script cannot run using FSL on Windows due to FSL dependency') if not os.environ.get('FSLDIR', ''): raise MRtrixError('Environment variable FSLDIR is not set; please run appropriate FSL configuration script') fast_cmd = fsl.exe_name('fast') app.warn('Use of fsl algorithm in dwibiascorrect script is discouraged due to its strong dependence ' + \ 'on brain masking (specifically its inability to correct voxels outside of this mask).' + \ 'Use of the ants algorithm is recommended for quantitative DWI analyses.') # Generate a mean b=0 image run.command('dwiextract in.mif - -bzero | mrmath - mean mean_bzero.mif -axis 3') # FAST doesn't accept a mask input; therefore need to explicitly mask the input image run.command('mrcalc mean_bzero.mif mask.mif -mult - | mrconvert - mean_bzero_masked.nii -strides -1,+2,+3') run.command(fast_cmd + ' -t 2 -o fast -n 3 -b mean_bzero_masked.nii') bias_path = fsl.find_image('fast_bias') # Rather than using a bias field estimate of 1.0 outside the brain mask, zero-fill the # output image outside of this mask run.command('mrcalc in.mif ' + bias_path + ' -div mask.mif -mult result.mif') run.command('mrconvert result.mif ' + path.from_user(app.ARGS.output), mrconvert_keyval=path.from_user(app.ARGS.input, False), force=app.FORCE_OVERWRITE) if app.ARGS.bias: run.command('mrconvert ' + bias_path + ' ' + path.from_user(app.ARGS.bias), mrconvert_keyval=path.from_user(app.ARGS.input, False), force=app.FORCE_OVERWRITE)
def _shebang(item): from mrtrix3 import app, utils #pylint: disable=import-outside-toplevel # If a complete path has been provided rather than just a file name, don't perform any additional file search if os.sep in item: path = item else: path = version_match(item) if path == item: path = find_executable(exe_name(item)) if not path: app.debug('File \"' + item + '\": Could not find file to query') return [] # Read the first 1024 bytes of the file with open(path, 'rb') as file_in: data = file_in.read(1024) # Try to find the shebang line for line in data.splitlines(): # Are there any non-text characters? If so, it's a binary file, so no need to looking for a shebang try: line = str(line.decode('utf-8')) except: app.debug('File \"' + item + '\": Not a text file') return [] line = line.strip() if len(line) > 2 and line[0:2] == '#!': # Need to strip first in case there's a gap between the shebang symbol and the interpreter path shebang = line[2:].strip().split(' ') # On Windows, /usr/bin/env can't be easily found, and any direct interpreter path will have a similar issue. # Instead, manually find the right interpreter to call using distutils # Also if script is written in Python, try to execute it using the same interpreter as that currently running if os.path.basename(shebang[0]) == 'env': if len(shebang) < 2: app.warn('Invalid shebang in script file \"' + item + '\" (missing interpreter after \"env\")') return [] if shebang[1] == 'python': if not sys.executable: app.warn( 'Unable to self-identify Python interpreter; file \"' + item + '\" not guaranteed to execute on same version') return [] shebang = [sys.executable] + shebang[2:] app.debug('File \"' + item + '\": Using current Python interpreter') elif utils.is_windows(): shebang = [ os.path.abspath(find_executable(exe_name(shebang[1]))) ] + shebang[2:] elif utils.is_windows(): shebang = [ os.path.abspath( find_executable(exe_name(os.path.basename( shebang[0])))) ] + shebang[1:] app.debug('File \"' + item + '\": string \"' + line + '\": ' + str(shebang)) return shebang app.debug('File \"' + item + '\": No shebang found') return []
def suffix(): #pylint: disable=unused-variable import os from mrtrix3 import app global _suffix if _suffix: return _suffix fsl_output_type = os.environ.get('FSLOUTPUTTYPE', '') if fsl_output_type == 'NIFTI': app.debug('NIFTI -> .nii') _suffix = '.nii' elif fsl_output_type == 'NIFTI_GZ': app.debug('NIFTI_GZ -> .nii.gz') _suffix = '.nii.gz' elif fsl_output_type == 'NIFTI_PAIR': app.debug('NIFTI_PAIR -> .img') _suffix = '.img' elif fsl_output_type == 'NIFTI_PAIR_GZ': app.error( 'MRtrix3 does not support compressed NIFTI pairs; please change FSLOUTPUTTYPE environment variable' ) elif fsl_output_type: app.warn( 'Unrecognised value for environment variable FSLOUTPUTTYPE (\"' + fsl_output_type + '\"): Expecting compressed NIfTIs, but FSL commands may fail') _suffix = '.nii.gz' else: app.warn( 'Environment variable FSLOUTPUTTYPE not set; FSL commands may fail, or script may fail to locate FSL command outputs' ) _suffix = '.nii.gz' return _suffix
def get_inputs(): #pylint: disable=unused-variable mask_path = path.to_scratch('mask.mif', False) if os.path.exists(mask_path): app.warn('-mask option is ignored by algorithm \'manual\'') os.remove(mask_path) run.command('mrconvert ' + path.from_user(app.ARGS.in_voxels) + ' ' + path.to_scratch('in_voxels.mif')) if app.ARGS.dirs: run.command('mrconvert ' + path.from_user(app.ARGS.dirs) + ' ' + path.to_scratch('dirs.mif') + ' -strides 0,0,0,1')
def getInputs(): #pylint: disable=unused-variable import os from mrtrix3 import app, path, run mask_path = path.toTemp('mask.mif', False) if os.path.exists(mask_path): app.warn('-mask option is ignored by algorithm \'manual\'') os.remove(mask_path) run.command('mrconvert ' + path.fromUser(app.args.in_voxels, True) + ' ' + path.toTemp('in_voxels.mif', True)) if app.args.dirs: run.command('mrconvert ' + path.fromUser(app.args.dirs, True) + ' ' + path.toTemp('dirs.mif', True) + ' -strides 0,0,0,1')
def getInputs(): import os from mrtrix3 import app, path, run mask_path = path.toTemp('mask.mif', False) if os.path.exists(mask_path): app.warn('-mask option is ignored by algorithm \'manual\'') os.remove(mask_path) run.command('mrconvert ' + path.fromUser(app.args.in_voxels, True) + ' ' + path.toTemp('in_voxels.mif', True)) if app.args.dirs: run.command('mrconvert ' + path.fromUser(app.args.dirs, True) + ' ' + path.toTemp('dirs.mif', True) + ' -stride 0,0,0,1')
def exe_name(name): #pylint: disable=unused-variable from mrtrix3 import app #pylint: disable=import-outside-toplevel if find_executable(name): output = name elif find_executable('fsl5.0-' + name): output = 'fsl5.0-' + name app.warn('Using FSL binary \"' + output + '\" rather than \"' + name + '\"; suggest checking FSL installation') else: raise MRtrixError('Could not find FSL program \"' + name + '\"; please verify FSL install') app.debug(output) return output
def eddyBinary(cuda): import os from mrtrix3 import app from distutils.spawn import find_executable if cuda: if find_executable('eddy_cuda'): app.debug('Selecting CUDA version of eddy') return 'eddy_cuda' else: app.warn('CUDA version of eddy not found; running standard version') if find_executable('eddy_openmp'): path = 'eddy_openmp' elif find_executable('eddy'): path = 'eddy' elif find_executable('fsl5.0-eddy'): path = 'fsl5.0-eddy' else: app.error('Could not find FSL program eddy; please verify FSL install') app.debug(path) return path
def suffix(): import os from mrtrix3 import app fsl_output_type = os.environ.get('FSLOUTPUTTYPE', '') if fsl_output_type == 'NIFTI': app.debug('NIFTI -> .nii') return '.nii' if fsl_output_type == 'NIFTI_GZ': app.debug('NIFTI_GZ -> .nii.gz') return '.nii.gz' if fsl_output_type == 'NIFTI_PAIR': app.debug('NIFTI_PAIR -> .img') return '.img' if fsl_output_type == 'NIFTI_PAIR_GZ': app.error( 'MRtrix3 does not support compressed NIFTI pairs; please change FSLOUTPUTTYPE environment variable' ) app.warn( 'Environment variable FSLOUTPUTTYPE not set; FSL commands may fail, or script may fail to locate FSL command outputs' ) return '.nii.gz'
def execute(): import math, os, shutil from mrtrix3 import app, image, path, run # Ideally want to use the oversampling-based regridding of the 5TT image from the SIFT model, not mrtransform # May need to commit 5ttregrid... # Verify input 5tt image run.command('5ttcheck 5tt.mif', False) # Get shell information shells = [ int(round(float(x))) for x in image.headerField('dwi.mif', 'shells').split() ] if len(shells) < 3: app.warn( 'Less than three b-value shells; response functions will not be applicable in resolving three tissues using MSMT-CSD algorithm' ) # Get lmax information (if provided) wm_lmax = [] if app.args.lmax: wm_lmax = [int(x.strip()) for x in app.args.lmax.split(',')] if not len(wm_lmax) == len(shells): app.error('Number of manually-defined lmax\'s (' + str(len(wm_lmax)) + ') does not match number of b-value shells (' + str(len(shells)) + ')') for l in wm_lmax: if l % 2: app.error('Values for lmax must be even') if l < 0: app.error('Values for lmax must be non-negative') run.command( 'dwi2tensor dwi.mif - -mask mask.mif | tensor2metric - -fa fa.mif -vector vector.mif' ) if not os.path.exists('dirs.mif'): run.function(shutil.copy, 'vector.mif', 'dirs.mif') run.command( 'mrtransform 5tt.mif 5tt_regrid.mif -template fa.mif -interp linear') # Basic tissue masks run.command( 'mrconvert 5tt_regrid.mif - -coord 3 2 -axes 0,1,2 | mrcalc - ' + str(app.args.pvf) + ' -gt mask.mif -mult wm_mask.mif') run.command( 'mrconvert 5tt_regrid.mif - -coord 3 0 -axes 0,1,2 | mrcalc - ' + str(app.args.pvf) + ' -gt fa.mif ' + str(app.args.fa) + ' -lt -mult mask.mif -mult gm_mask.mif') run.command( 'mrconvert 5tt_regrid.mif - -coord 3 3 -axes 0,1,2 | mrcalc - ' + str(app.args.pvf) + ' -gt fa.mif ' + str(app.args.fa) + ' -lt -mult mask.mif -mult csf_mask.mif') # Revise WM mask to only include single-fibre voxels app.console( 'Calling dwi2response recursively to select WM single-fibre voxels using \'' + app.args.wm_algo + '\' algorithm') recursive_cleanup_option = '' if not app._cleanup: recursive_cleanup_option = ' -nocleanup' run.command( 'dwi2response ' + app.args.wm_algo + ' dwi.mif wm_ss_response.txt -mask wm_mask.mif -voxels wm_sf_mask.mif -tempdir ' + app._tempDir + recursive_cleanup_option) # Check for empty masks wm_voxels = int( image.statistic('wm_sf_mask.mif', 'count', 'wm_sf_mask.mif')) gm_voxels = int(image.statistic('gm_mask.mif', 'count', 'gm_mask.mif')) csf_voxels = int(image.statistic('csf_mask.mif', 'count', 'csf_mask.mif')) empty_masks = [] if not wm_voxels: empty_masks.append('WM') if not gm_voxels: empty_masks.append('GM') if not csf_voxels: empty_masks.append('CSF') if empty_masks: message = ','.join(empty_masks) message += ' tissue mask' if len(empty_masks) > 1: message += 's' message += ' empty; cannot estimate response function' if len(empty_masks) > 1: message += 's' app.error(message) # For each of the three tissues, generate a multi-shell response bvalues_option = ' -shell ' + ','.join(map(str, shells)) sfwm_lmax_option = '' if wm_lmax: sfwm_lmax_option = ' -lmax ' + ','.join(map(str, wm_lmax)) run.command('amp2response dwi.mif wm_sf_mask.mif dirs.mif wm.txt' + bvalues_option + sfwm_lmax_option) run.command('amp2response dwi.mif gm_mask.mif dirs.mif gm.txt' + bvalues_option + ' -isotropic') run.command('amp2response dwi.mif csf_mask.mif dirs.mif csf.txt' + bvalues_option + ' -isotropic') run.function(shutil.copyfile, 'wm.txt', path.fromUser(app.args.out_wm, False)) run.function(shutil.copyfile, 'gm.txt', path.fromUser(app.args.out_gm, False)) run.function(shutil.copyfile, 'csf.txt', path.fromUser(app.args.out_csf, False)) # Generate output 4D binary image with voxel selections; RGB as in MSMT-CSD paper run.command( 'mrcat csf_mask.mif gm_mask.mif wm_sf_mask.mif voxels.mif -axis 3')
def command(cmd, exitOnError=True): #pylint: disable=unused-variable import inspect, itertools, shlex, signal, string, subprocess, sys, tempfile from distutils.spawn import find_executable from mrtrix3 import app # This is the only global variable that is _modified_ within this function global _processes # Vectorise the command string, preserving anything encased within quotation marks if os.sep == '/': # Cheap POSIX compliance check cmdsplit = shlex.split(cmd) else: # Native Windows Python cmdsplit = [ entry.strip('\"') for entry in shlex.split(cmd, posix=False) ] if _lastFile: if _triggerContinue(cmdsplit): app.debug( 'Detected last file in command \'' + cmd + '\'; this is the last run.command() / run.function() call that will be skipped' ) if app.verbosity: sys.stderr.write(app.colourExec + 'Skipping command:' + app.colourClear + ' ' + cmd + '\n') sys.stderr.flush() return ('', '') # This splits the command string based on the piping character '|', such that each # individual executable (along with its arguments) appears as its own list cmdstack = [ list(g) for k, g in itertools.groupby(cmdsplit, lambda s: s != '|') if k ] for line in cmdstack: is_mrtrix_exe = line[0] in _mrtrix_exe_list if is_mrtrix_exe: line[0] = versionMatch(line[0]) if app.numThreads is not None: line.extend(['-nthreads', str(app.numThreads)]) # Get MRtrix3 binaries to output additional INFO-level information if running in debug mode if app.verbosity == 3: line.append('-info') elif not app.verbosity: line.append('-quiet') else: line[0] = exeName(line[0]) shebang = _shebang(line[0]) if shebang: if not is_mrtrix_exe: # If a shebang is found, and this call is therefore invoking an # interpreter, can't rely on the interpreter finding the script # from PATH; need to find the full path ourselves. line[0] = find_executable(line[0]) for item in reversed(shebang): line.insert(0, item) app.debug('To execute: ' + str(cmdstack)) if app.verbosity: sys.stderr.write(app.colourExec + 'Command:' + app.colourClear + ' ' + cmd + '\n') sys.stderr.flush() # Disable interrupt signal handler while threads are running try: signal.signal(signal.SIGINT, signal.default_int_handler) except: pass # Construct temporary text files for holding stdout / stderr contents when appropriate # (One entry per process; each is a tuple containing two entries, each of which is either a # file-like object, or None) tempfiles = [] # Execute all processes assert not _processes for index, to_execute in enumerate(cmdstack): file_out = None file_err = None # If there's at least one command prior to this, need to receive the stdout from the prior command # at the stdin of this command; otherwise, nothing to receive if index > 0: handle_in = _processes[index - 1].stdout else: handle_in = None # If this is not the last command, then stdout needs to be piped to the next command; # otherwise, write stdout to a temporary file so that the contents can be read later if index < len(cmdstack) - 1: handle_out = subprocess.PIPE else: file_out = tempfile.TemporaryFile() handle_out = file_out.fileno() # If we're in debug / info mode, the contents of stderr will be read and printed to the terminal # as the command progresses, hence this needs to go to a pipe; otherwise, write it to a temporary # file so that the contents can be read later if app.verbosity > 1: handle_err = subprocess.PIPE else: file_err = tempfile.TemporaryFile() handle_err = file_err.fileno() # Set off the processes try: try: process = subprocess.Popen(to_execute, stdin=handle_in, stdout=handle_out, stderr=handle_err, env=_env, preexec_fn=os.setpgrp) # pylint: disable=bad-option-value,subprocess-popen-preexec-fn except AttributeError: process = subprocess.Popen(to_execute, stdin=handle_in, stdout=handle_out, stderr=handle_err, env=_env) _processes.append(process) tempfiles.append((file_out, file_err)) # FileNotFoundError not defined in Python 2.7 except OSError as e: if exitOnError: app.error('\'' + to_execute[0] + '\' not executed ("' + str(e) + '"); script cannot proceed') else: app.warn('\'' + to_execute[0] + '\' not executed ("' + str(e) + '")') for p in _processes: p.terminate() _processes = [] break return_stdout = '' return_stderr = '' error = False error_text = '' # Wait for all commands to complete # Switch how we monitor running processes / wait for them to complete # depending on whether or not the user has specified -info or -debug option try: if app.verbosity > 1: for process in _processes: stderrdata = b'' do_indent = True while True: # Have to read one character at a time: Waiting for a newline character using e.g. readline() will prevent MRtrix progressbars from appearing byte = process.stderr.read(1) stderrdata += byte char = byte.decode('cp1252', errors='ignore') if not char and process.poll() is not None: break if do_indent and char in string.printable and char != '\r' and char != '\n': sys.stderr.write(' ') do_indent = False elif char in ['\r', '\n']: do_indent = True sys.stderr.write(char) sys.stderr.flush() stderrdata = stderrdata.decode('utf-8', errors='replace') return_stderr += stderrdata if process.returncode: error = True error_text += stderrdata else: for process in _processes: process.wait() except (KeyboardInterrupt, SystemExit): app.handler(signal.SIGINT, inspect.currentframe()) # Re-enable interrupt signal handler try: signal.signal(signal.SIGINT, app.handler) except: pass # For any command stdout / stderr data that wasn't either passed to another command or # printed to the terminal during execution, read it here. for index in range(len(cmdstack)): if tempfiles[index][0] is not None: tempfiles[index][0].flush() tempfiles[index][0].seek(0) stdout_text = tempfiles[index][0].read().decode('utf-8', errors='replace') return_stdout += stdout_text if _processes[index].returncode: error = True error_text += stdout_text if tempfiles[index][1] is not None: tempfiles[index][1].flush() tempfiles[index][1].seek(0) stderr_text = tempfiles[index][1].read().decode('utf-8', errors='replace') return_stderr += stderr_text if _processes[index].returncode: error = True error_text += stderr_text _processes = [] if error: if exitOnError: app.cleanup = False caller = inspect.getframeinfo(inspect.stack()[1][0]) script_name = os.path.basename(sys.argv[0]) app.console('') try: filename = caller.filename lineno = caller.lineno except AttributeError: filename = caller[1] lineno = caller[2] sys.stderr.write(script_name + ': ' + app.colourError + '[ERROR] Command failed: ' + cmd + app.colourClear + app.colourDebug + ' (' + os.path.basename(filename) + ':' + str(lineno) + ')' + app.colourClear + '\n') sys.stderr.write(script_name + ': ' + app.colourConsole + 'Output of failed command:' + app.colourClear + '\n') for line in error_text.splitlines(): sys.stderr.write(' ' * (len(script_name) + 2) + line + '\n') app.console('') sys.stderr.flush() if app.tempDir: with open(os.path.join(app.tempDir, 'error.txt'), 'w') as outfile: outfile.write(cmd + '\n\n' + error_text + '\n') app.complete() sys.exit(1) else: app.warn('Command failed: ' + cmd) # Only now do we append to the script log, since the command has completed successfully # Note: Writing the command as it was formed as the input to run.command(): # other flags may potentially change if this file is eventually used to resume the script if app.tempDir: with open(os.path.join(app.tempDir, 'log.txt'), 'a') as outfile: outfile.write(cmd + '\n') return (return_stdout, return_stderr)
def runSubject(bids_dir, label, output_prefix): output_dir = os.path.join(output_prefix, label) if os.path.exists(output_dir): shutil.rmtree(output_dir) os.makedirs(output_dir) os.makedirs(os.path.join(output_dir, 'connectome')) os.makedirs(os.path.join(output_dir, 'dwi')) fsl_path = os.environ.get('FSLDIR', '') if not fsl_path: app.error( 'Environment variable FSLDIR is not set; please run appropriate FSL configuration script' ) flirt_cmd = fsl.exeName('flirt') fslanat_cmd = fsl.exeName('fsl_anat') fsl_suffix = fsl.suffix() unring_cmd = 'unring.a64' if not find_executable(unring_cmd): app.console('Command \'' + unring_cmd + '\' not found; cannot perform Gibbs ringing removal') unring_cmd = '' dwibiascorrect_algo = '-ants' if not find_executable('N4BiasFieldCorrection'): # Can't use findFSLBinary() here, since we want to proceed even if it's not found if find_executable('fast') or find_executable('fsl5.0-fast'): dwibiascorrect_algo = '-fsl' app.console('Could not find ANTs program N4BiasFieldCorrection; ' 'using FSL FAST for bias field correction') else: dwibiascorrect_algo = '' app.warn( 'Could not find ANTs program \'N4BiasFieldCorrection\' or FSL program \'fast\'; ' 'will proceed without performing DWI bias field correction') if not app.args.parcellation: app.error( 'For participant-level analysis, desired parcellation must be provided using the -parcellation option' ) parc_image_path = '' parc_lut_file = '' mrtrix_lut_file = os.path.join( os.path.dirname(os.path.abspath(app.__file__)), os.pardir, os.pardir, 'share', 'mrtrix3', 'labelconvert') if app.args.parcellation == 'fs_2005' or app.args.parcellation == 'fs_2009': if not 'FREESURFER_HOME' in os.environ: app.error( 'Environment variable FREESURFER_HOME not set; please verify FreeSurfer installation' ) if not find_executable('recon-all'): app.error( 'Could not find FreeSurfer script recon-all; please verify FreeSurfer installation' ) parc_lut_file = os.path.join(os.environ['FREESURFER_HOME'], 'FreeSurferColorLUT.txt') if app.args.parcellation == 'fs_2005': mrtrix_lut_file = os.path.join(mrtrix_lut_file, 'fs_default.txt') else: mrtrix_lut_file = os.path.join(mrtrix_lut_file, 'fs_a2009s.txt') if app.args.parcellation == 'aal' or app.args.parcellation == 'aal2': mni152_path = os.path.join(fsl_path, 'data', 'standard', 'MNI152_T1_1mm.nii.gz') if not os.path.isfile(mni152_path): app.error( 'Could not find MNI152 template image within FSL installation (expected location: ' + mni152_path + ')') if app.args.parcellation == 'aal': parc_image_path = os.path.abspath( os.path.join(os.sep, 'opt', 'aal', 'ROI_MNI_V4.nii')) parc_lut_file = os.path.abspath( os.path.join(os.sep, 'opt', 'aal', 'ROI_MNI_V4.txt')) mrtrix_lut_file = os.path.join(mrtrix_lut_file, 'aal.txt') else: parc_image_path = os.path.abspath( os.path.join(os.sep, 'opt', 'aal', 'ROI_MNI_V5.nii')) parc_lut_file = os.path.abspath( os.path.join(os.sep, 'opt', 'aal', 'ROI_MNI_V5.txt')) mrtrix_lut_file = os.path.join(mrtrix_lut_file, 'aal2.txt') if parc_image_path and not os.path.isfile(parc_image_path): if app.args.atlas_path: parc_image_path = [ parc_image_path, os.path.join(os.path.dirname(app.args.atlas_path), os.path.basename(parc_image_path)) ] if os.path.isfile(parc_image_path[1]): parc_image_path = parc_image_path[1] else: app.error( 'Could not find parcellation image (tested locations: ' + str(parc_image_path) + ')') else: app.error( 'Could not find parcellation image (expected location: ' + parc_image_path + ')') if not os.path.isfile(parc_lut_file): if app.args.atlas_path: parc_lut_file = [ parc_lut_file, os.path.join(os.path.dirname(app.args.atlas_path), os.path.basename(parc_lut_file)) ] if os.path.isfile(parc_lut_file[1]): parc_lut_file = parc_lut_file[1] else: app.error( 'Could not find parcellation lookup table file (tested locations: ' + str(parc_lut_file) + ')') else: app.error( 'Could not find parcellation lookup table file (expected location: ' + parc_lut_file + ')') if not os.path.exists(mrtrix_lut_file): app.error( 'Could not find MRtrix3 connectome lookup table file (expected location: ' + mrtrix_lut_file + ')') app.makeTempDir() # Need to perform an initial import of JSON data using mrconvert; so let's grab the diffusion gradient table as well # If no bvec/bval present, need to go down the directory listing # Only try to import JSON file if it's actually present # direction in the acquisition they'll need to be split across multiple files # May need to concatenate more than one input DWI, since if there's more than one phase-encode direction # in the acquired DWIs (i.e. not just those used for estimating the inhomogeneity field), they will # need to be stored as separate NIfTI files in the 'dwi/' directory. dwi_image_list = glob.glob( os.path.join(bids_dir, label, 'dwi', label) + '*_dwi.nii*') dwi_index = 1 for entry in dwi_image_list: # os.path.split() falls over with .nii.gz extensions; only removes the .gz prefix = entry.split(os.extsep)[0] if os.path.isfile(prefix + '.bval') and os.path.isfile(prefix + '.bvec'): prefix = prefix + '.' else: prefix = os.path.join(bids_dir, 'dwi') if not (os.path.isfile(prefix + 'bval') and os.path.isfile(prefix + 'bvec')): app.error( 'Unable to locate valid diffusion gradient table for image \'' + entry + '\'') grad_import_option = ' -fslgrad ' + prefix + 'bvec ' + prefix + 'bval' json_path = prefix + 'json' if os.path.isfile(json_path): json_import_option = ' -json_import ' + json_path else: json_import_option = '' run.command('mrconvert ' + entry + grad_import_option + json_import_option + ' ' + path.toTemp('dwi' + str(dwi_index) + '.mif', True)) dwi_index += 1 # Go hunting for reversed phase-encode data dedicated to field map estimation fmap_image_list = [] fmap_dir = os.path.join(bids_dir, label, 'fmap') fmap_index = 1 if os.path.isdir(fmap_dir): if app.args.preprocessed: app.error('fmap/ directory detected for subject \'' + label + '\' despite use of ' + option_prefix + 'preprocessed option') fmap_image_list = glob.glob( os.path.join(fmap_dir, label) + '_dir-*_epi.nii*') for entry in fmap_image_list: prefix = entry.split(os.extsep)[0] json_path = prefix + '.json' with open(json_path, 'r') as f: json_elements = json.load(f) if 'IntendedFor' in json_elements and not any( i.endswith(json_elements['IntendedFor']) for i in dwi_image_list): app.console('Image \'' + entry + '\' is not intended for use with DWIs; skipping') continue if os.path.isfile(json_path): json_import_option = ' -json_import ' + json_path # fmap files will not come with any gradient encoding in the JSON; # therefore we need to add it manually ourselves so that mrcat / mrconvert can # appropriately handle the table once these images are concatenated with the DWIs fmap_image_size = image.Header(entry).size() fmap_image_num_volumes = 1 if len( fmap_image_size) == 3 else fmap_image_size[3] run.command('mrconvert ' + entry + json_import_option + ' -set_property dw_scheme \"' + '\\n'.join(['0,0,1,0'] * fmap_image_num_volumes) + '\" ' + path.toTemp('fmap' + str(fmap_index) + '.mif', True)) fmap_index += 1 else: app.warn('No corresponding .json file found for image \'' + entry + '\'; skipping') fmap_image_list = [ 'fmap' + str(index) + '.mif' for index in range(1, fmap_index) ] # If there's no data in fmap/ directory, need to check to see if there's any phase-encoding # contrast within the input DWI(s) elif len(dwi_image_list) < 2 and not app.args.preprocessed: app.error( 'Inadequate data for pre-processing of subject \'' + label + '\': No phase-encoding contrast in input DWIs or fmap/ directory') dwi_image_list = [ 'dwi' + str(index) + '.mif' for index in range(1, dwi_index) ] # Import anatomical image run.command('mrconvert ' + os.path.join(bids_dir, label, 'anat', label + '_T1w.nii.gz') + ' ' + path.toTemp('T1.mif', True)) cwd = os.getcwd() app.gotoTempDir() dwipreproc_se_epi = '' dwipreproc_se_epi_option = '' # For automated testing, down-sampled images are used. However, this invalidates the requirements of # both MP-PCA denoising and Gibbs ringing removal. In addition, eddy can still take a long time # despite the down-sampling. Therefore, provide images that have been pre-processed to the stage # where it is still only DWI, JSON & bvecs/bvals that need to be provided. if app.args.preprocessed: if len(dwi_image_list) > 1: app.error( 'If DWIs have been pre-processed, then only a single DWI file should need to be provided' ) app.console( 'Skipping MP-PCA denoising, ' + ('Gibbs ringing removal, ' if unring_cmd else '') + 'distortion correction and bias field correction due to use of ' + option_prefix + 'preprocessed option') run.function(os.rename, dwi_image_list[0], 'dwi.mif') else: # Do initial image pre-processing (denoising, Gibbs ringing removal if available, distortion correction & bias field correction) as normal # Concatenate any SE EPI images with the DWIs before denoising (& unringing), then # separate them again after the fact dwidenoise_input = 'dwidenoise_input.mif' fmap_num_volumes = 0 if fmap_image_list: run.command('mrcat ' + ' '.join(fmap_image_list) + ' fmap_cat.mif -axis 3') for i in fmap_image_list: file.delTemporary(i) fmap_num_volumes = image.Header('fmap_cat.mif').size()[3] dwidenoise_input = 'all_cat.mif' run.command('mrcat fmap_cat.mif ' + ' '.join(dwi_image_list) + ' ' + dwidenoise_input + ' -axis 3') file.delTemporary('fmap_cat.mif') else: # Even if no explicit fmap images, may still need to concatenate multiple DWI inputs if len(dwi_image_list) > 1: run.command('mrcat ' + ' '.join(dwi_image_list) + ' ' + dwidenoise_input + ' -axis 3') else: run.function(shutil.move, dwi_image_list[0], dwidenoise_input) for i in dwi_image_list: file.delTemporary(i) # Step 1: Denoise run.command('dwidenoise ' + dwidenoise_input + ' dwi_denoised.' + ('nii' if unring_cmd else 'mif')) if unring_cmd: run.command('mrinfo ' + dwidenoise_input + ' -json_keyval input.json') file.delTemporary(dwidenoise_input) # Step 2: Gibbs ringing removal (if available) if unring_cmd: run.command(unring_cmd + ' dwi_denoised.nii dwi_unring' + fsl_suffix + ' -n 100') file.delTemporary('dwi_denoised.nii') unring_output_path = fsl.findImage('dwi_unring') run.command('mrconvert ' + unring_output_path + ' dwi_unring.mif -json_import input.json') file.delTemporary(unring_output_path) file.delTemporary('input.json') # If fmap images and DWIs have been concatenated, now is the time to split them back apart dwipreproc_input = 'dwi_unring.mif' if unring_cmd else 'dwi_denoised.mif' if fmap_num_volumes: cat_input = 'dwi_unring.mif' if unring_cmd else 'dwi_denoised.mif' dwipreproc_se_epi = 'se_epi.mif' run.command('mrconvert ' + cat_input + ' ' + dwipreproc_se_epi + ' -coord 3 0:' + str(fmap_num_volumes - 1)) cat_num_volumes = image.Header(cat_input).size()[3] run.command('mrconvert ' + cat_input + ' dwipreproc_in.mif -coord 3 ' + str(fmap_num_volumes) + ':' + str(cat_num_volumes - 1)) file.delTemporary(dwipreproc_input) dwipreproc_input = 'dwipreproc_in.mif' dwipreproc_se_epi_option = ' -se_epi ' + dwipreproc_se_epi # Step 3: Distortion correction run.command('dwipreproc ' + dwipreproc_input + ' dwi_preprocessed.mif -rpe_header' + dwipreproc_se_epi_option) file.delTemporary(dwipreproc_input) if dwipreproc_se_epi: file.delTemporary(dwipreproc_se_epi) # Step 4: Bias field correction if dwibiascorrect_algo: run.command('dwibiascorrect dwi_preprocessed.mif dwi.mif ' + dwibiascorrect_algo) file.delTemporary('dwi_preprocessed.mif') else: run.function(shutil.move, 'dwi_preprocessed.mif', 'dwi.mif') # No longer branching based on whether or not -preprocessed was specified # Step 5: Generate a brain mask for DWI run.command('dwi2mask dwi.mif dwi_mask.mif') # Step 6: Perform brain extraction on the T1 image in its original space # (this is necessary for histogram matching prior to registration) # Use fsl_anat script run.command('mrconvert T1.mif T1.nii -stride -1,+2,+3') run.command(fslanat_cmd + ' -i T1.nii --noseg --nosubcortseg') run.command('mrconvert ' + fsl.findImage('T1.anat' + os.sep + 'T1_biascorr_brain_mask') + ' T1_mask.mif -datatype bit') run.command('mrconvert ' + fsl.findImage('T1.anat' + os.sep + 'T1_biascorr_brain') + ' T1_biascorr_brain.mif') file.delTemporary('T1.anat') # Step 7: Generate target images for T1->DWI registration run.command('dwiextract dwi.mif -bzero - | ' 'mrcalc - 0.0 -max - | ' 'mrmath - mean -axis 3 dwi_meanbzero.mif') run.command( 'mrcalc 1 dwi_meanbzero.mif -div dwi_mask.mif -mult - | ' 'mrhistmatch - T1_biascorr_brain.mif dwi_pseudoT1.mif -mask_input dwi_mask.mif -mask_target T1_mask.mif' ) run.command( 'mrcalc 1 T1_biascorr_brain.mif -div T1_mask.mif -mult - | ' 'mrhistmatch - dwi_meanbzero.mif T1_pseudobzero.mif -mask_input T1_mask.mif -mask_target dwi_mask.mif' ) # Step 8: Perform T1->DWI registration # Note that two registrations are performed: Even though we have a symmetric registration, # generation of the two histogram-matched images means that you will get slightly different # answers depending on which synthesized image & original image you use. run.command( 'mrregister T1_biascorr_brain.mif dwi_pseudoT1.mif -type rigid -mask1 T1_mask.mif -mask2 dwi_mask.mif -rigid rigid_T1_to_pseudoT1.txt' ) file.delTemporary('T1_biascorr_brain.mif') run.command( 'mrregister T1_pseudobzero.mif dwi_meanbzero.mif -type rigid -mask1 T1_mask.mif -mask2 dwi_mask.mif -rigid rigid_pseudobzero_to_bzero.txt' ) file.delTemporary('dwi_meanbzero.mif') run.command( 'transformcalc rigid_T1_to_pseudoT1.txt rigid_pseudobzero_to_bzero.txt average rigid_T1_to_dwi.txt' ) file.delTemporary('rigid_T1_to_pseudoT1.txt') file.delTemporary('rigid_pseudobzero_to_bzero.txt') run.command( 'mrtransform T1.mif T1_registered.mif -linear rigid_T1_to_dwi.txt') file.delTemporary('T1.mif') # Note: Since we're using a mask from fsl_anat (which crops the FoV), but using it as input to 5ttge fsl # (which is receiving the raw T1), we need to resample in order to have the same dimensions between these two run.command( 'mrtransform T1_mask.mif T1_mask_registered.mif -linear rigid_T1_to_dwi.txt -template T1_registered.mif -interp nearest' ) file.delTemporary('T1_mask.mif') # Step 9: Generate 5TT image for ACT run.command( '5ttgen fsl T1_registered.mif 5TT.mif -mask T1_mask_registered.mif') file.delTemporary('T1_mask_registered.mif') # Step 10: Estimate response functions for spherical deconvolution run.command( 'dwi2response dhollander dwi.mif response_wm.txt response_gm.txt response_csf.txt -mask dwi_mask.mif' ) # Step 11: Determine whether we are working with single-shell or multi-shell data shells = [ int(round(float(value))) for value in image.mrinfo('dwi.mif', 'shellvalues').strip().split() ] multishell = (len(shells) > 2) # Step 12: Perform spherical deconvolution # Use a dilated mask for spherical deconvolution as a 'safety margin' - # ACT should be responsible for stopping streamlines before they reach the edge of the DWI mask run.command('maskfilter dwi_mask.mif dilate dwi_mask_dilated.mif -npass 3') if multishell: run.command( 'dwi2fod msmt_csd dwi.mif response_wm.txt FOD_WM.mif response_gm.txt FOD_GM.mif response_csf.txt FOD_CSF.mif ' '-mask dwi_mask_dilated.mif -lmax 10,0,0') file.delTemporary('FOD_GM.mif') file.delTemporary('FOD_CSF.mif') else: # Still use the msmt_csd algorithm with single-shell data: Use hard non-negativity constraint # Also incorporate the CSF response to provide some fluid attenuation run.command( 'dwi2fod msmt_csd dwi.mif response_wm.txt FOD_WM.mif response_csf.txt FOD_CSF.mif ' '-mask dwi_mask_dilated.mif -lmax 10,0') file.delTemporary('FOD_CSF.mif') # Step 13: Generate the grey matter parcellation # The necessary steps here will vary significantly depending on the parcellation scheme selected run.command( 'mrconvert T1_registered.mif T1_registered.nii -stride +1,+2,+3') if app.args.parcellation == 'fs_2005' or app.args.parcellation == 'fs_2009': # Run FreeSurfer pipeline on this subject's T1 image run.command('recon-all -sd ' + app.tempDir + ' -subjid freesurfer -i T1_registered.nii') run.command('recon-all -sd ' + app.tempDir + ' -subjid freesurfer -all') # Grab the relevant parcellation image and target lookup table for conversion parc_image_path = os.path.join('freesurfer', 'mri') if app.args.parcellation == 'fs_2005': parc_image_path = os.path.join(parc_image_path, 'aparc+aseg.mgz') else: parc_image_path = os.path.join(parc_image_path, 'aparc.a2009s+aseg.mgz') # Perform the index conversion run.command('labelconvert ' + parc_image_path + ' ' + parc_lut_file + ' ' + mrtrix_lut_file + ' parc_init.mif') if app.cleanup: run.function(shutil.rmtree, 'freesurfer') # Fix the sub-cortical grey matter parcellations using FSL FIRST run.command('labelsgmfix parc_init.mif T1_registered.mif ' + mrtrix_lut_file + ' parc.mif') file.delTemporary('parc_init.mif') elif app.args.parcellation == 'aal' or app.args.parcellation == 'aal2': # Can use MNI152 image provided with FSL for registration run.command(flirt_cmd + ' -ref ' + mni152_path + ' -in T1_registered.nii -omat T1_to_MNI_FLIRT.mat -dof 12') run.command('transformconvert T1_to_MNI_FLIRT.mat T1_registered.nii ' + mni152_path + ' flirt_import T1_to_MNI_MRtrix.mat') file.delTemporary('T1_to_MNI_FLIRT.mat') run.command( 'transformcalc T1_to_MNI_MRtrix.mat invert MNI_to_T1_MRtrix.mat') file.delTemporary('T1_to_MNI_MRtrix.mat') run.command('mrtransform ' + parc_image_path + ' AAL.mif -linear MNI_to_T1_MRtrix.mat ' '-template T1_registered.mif -interp nearest') file.delTemporary('MNI_to_T1_MRtrix.mat') run.command('labelconvert AAL.mif ' + parc_lut_file + ' ' + mrtrix_lut_file + ' parc.mif') file.delTemporary('AAL.mif') else: app.error('Unknown parcellation scheme requested: ' + app.args.parcellation) file.delTemporary('T1_registered.nii') # Step 14: Generate the tractogram # If not manually specified, determine the appropriate number of streamlines based on the number of nodes in the parcellation: # mean edge weight of 1,000 streamlines # A smaller FOD amplitude threshold of 0.06 (default 0.1) is used for tracking due to the use of the msmt_csd # algorithm, which imposes a hard rather than soft non-negativity constraint num_nodes = int(image.statistic('parc.mif', 'max')) num_streamlines = 1000 * num_nodes * num_nodes if app.args.streamlines: num_streamlines = app.args.streamlines run.command( 'tckgen FOD_WM.mif tractogram.tck -act 5TT.mif -backtrack -crop_at_gmwmi -cutoff 0.06 -maxlength 250 -power 0.33 ' '-select ' + str(num_streamlines) + ' -seed_dynamic FOD_WM.mif') # Step 15: Use SIFT2 to determine streamline weights fd_scale_gm_option = '' if not multishell: fd_scale_gm_option = ' -fd_scale_gm' run.command( 'tcksift2 tractogram.tck FOD_WM.mif weights.csv -act 5TT.mif -out_mu mu.txt' + fd_scale_gm_option) # Step 16: Generate a TDI (to verify that SIFT2 has worked correctly) with open('mu.txt', 'r') as f: mu = float(f.read()) run.command( 'tckmap tractogram.tck -tck_weights_in weights.csv -template FOD_WM.mif -precise - | ' 'mrcalc - ' + str(mu) + ' -mult tdi.mif') # Step 17: Generate the connectome # Only provide the standard density-weighted connectome for now run.command( 'tck2connectome tractogram.tck parc.mif connectome.csv -tck_weights_in weights.csv' ) file.delTemporary('weights.csv') # Move necessary files to output directory run.function( shutil.copy, 'connectome.csv', os.path.join(output_dir, 'connectome', label + '_connectome.csv')) run.command('mrconvert dwi.mif ' + os.path.join(output_dir, 'dwi', label + '_dwi.nii.gz') + ' -export_grad_fsl ' + os.path.join(output_dir, 'dwi', label + '_dwi.bvec') + ' ' + os.path.join(output_dir, 'dwi', label + '_dwi.bval') + ' -json_export ' + os.path.join(output_dir, 'dwi', label + '_dwi.json')) run.command('mrconvert tdi.mif ' + os.path.join(output_dir, 'dwi', label + '_tdi.nii.gz')) run.function(shutil.copy, 'mu.txt', os.path.join(output_dir, 'connectome', label + '_mu.txt')) run.function(shutil.copy, 'response_wm.txt', os.path.join(output_dir, 'dwi', label + '_response.txt')) # Manually wipe and zero the temp directory (since we might be processing more than one subject) os.chdir(cwd) if app.cleanup: app.console('Deleting temporary directory ' + app.tempDir) # Can't use run.function() here; it'll try to write to the log file that resides in the temp directory just deleted shutil.rmtree(app.tempDir) else: app.console('Contents of temporary directory kept, location: ' + app.tempDir) app.tempDir = ''
) participant_options.add_argument( option_prefix + 'streamlines', type=int, help='The number of streamlines to generate for each subject') app.parse() if app.isWindows(): app.error('Script cannot be run on Windows due to FSL dependency') if find_executable('bids-validator'): run.command('bids-validator ' + app.args.bids_dir) else: app.warn( 'BIDS validator script not installed; proceeding without validation of input data' ) # Running participant level if app.args.analysis_level == 'participant': subjects_to_analyze = [] # Only run a subset of subjects if app.args.participant_label: subjects_to_analyze = [ 'sub-' + sub_index for sub_index in app.args.participant_label ] for subject_dir in subjects_to_analyze: if not os.path.isdir(os.path.join(app.args.bids_dir, subject_dir)): app.error('Unable to find directory for subject: ' + subject_dir)
def execute(): #pylint: disable=unused-variable import math, os from mrtrix3 import app, fsl, image, run if app.isWindows(): app.error('\'fsl\' algorithm of 5ttgen script cannot be run on Windows: FSL not available on Windows') fsl_path = os.environ.get('FSLDIR', '') if not fsl_path: app.error('Environment variable FSLDIR is not set; please run appropriate FSL configuration script') bet_cmd = fsl.exeName('bet') fast_cmd = fsl.exeName('fast') first_cmd = fsl.exeName('run_first_all') ssroi_cmd = fsl.exeName('standard_space_roi') first_atlas_path = os.path.join(fsl_path, 'data', 'first', 'models_336_bin') if not os.path.isdir(first_atlas_path): app.error('Atlases required for FSL\'s FIRST program not installed; please install fsl-first-data using your relevant package manager') fsl_suffix = fsl.suffix() sgm_structures = [ 'L_Accu', 'R_Accu', 'L_Caud', 'R_Caud', 'L_Pall', 'R_Pall', 'L_Puta', 'R_Puta', 'L_Thal', 'R_Thal' ] if app.args.sgm_amyg_hipp: sgm_structures.extend([ 'L_Amyg', 'R_Amyg', 'L_Hipp', 'R_Hipp' ]) t1_spacing = image.Header('input.mif').spacing() upsample_for_first = False # If voxel size is 1.25mm or larger, make a guess that the user has erroneously re-gridded their data if math.pow(t1_spacing[0] * t1_spacing[1] * t1_spacing[2], 1.0/3.0) > 1.225: app.warn('Voxel size larger than expected for T1-weighted images (' + str(t1_spacing) + '); ' 'note that ACT does not require re-gridding of T1 image to DWI space, and indeed ' 'retaining the original higher resolution of the T1 image is preferable') upsample_for_first = True run.command('mrconvert input.mif T1.nii -strides -1,+2,+3') fast_t1_input = 'T1.nii' fast_t2_input = '' # Decide whether or not we're going to do any brain masking if os.path.exists('mask.mif'): fast_t1_input = 'T1_masked' + fsl_suffix # Check to see if the mask matches the T1 image if image.match('T1.nii', 'mask.mif'): run.command('mrcalc T1.nii mask.mif -mult ' + fast_t1_input) mask_path = 'mask.mif' else: app.warn('Mask image does not match input image - re-gridding') run.command('mrtransform mask.mif mask_regrid.mif -template T1.nii -datatype bit') run.command('mrcalc T1.nii mask_regrid.mif -mult ' + fast_t1_input) mask_path = 'mask_regrid.mif' if os.path.exists('T2.nii'): fast_t2_input = 'T2_masked' + fsl_suffix run.command('mrcalc T2.nii ' + mask_path + ' -mult ' + fast_t2_input) elif app.args.premasked: fast_t1_input = 'T1.nii' if os.path.exists('T2.nii'): fast_t2_input = 'T2.nii' else: # Use FSL command standard_space_roi to do an initial masking of the image before BET # Also reduce the FoV of the image # Using MNI 1mm dilated brain mask rather than the -b option in standard_space_roi (which uses the 2mm mask); the latter looks 'buggy' to me... Unfortunately even with the 1mm 'dilated' mask, it can still cut into some brain areas, hence the explicit dilation mni_mask_path = os.path.join(fsl_path, 'data', 'standard', 'MNI152_T1_1mm_brain_mask_dil.nii.gz') mni_mask_dilation = 0 if os.path.exists (mni_mask_path): mni_mask_dilation = 4 else: mni_mask_path = os.path.join(fsl_path, 'data', 'standard', 'MNI152_T1_2mm_brain_mask_dil.nii.gz') if os.path.exists (mni_mask_path): mni_mask_dilation = 2 if mni_mask_dilation: run.command('maskfilter ' + mni_mask_path + ' dilate mni_mask.nii -npass ' + str(mni_mask_dilation)) if app.args.nocrop: ssroi_roi_option = ' -roiNONE' else: ssroi_roi_option = ' -roiFOV' run.command(ssroi_cmd + ' T1.nii T1_preBET' + fsl_suffix + ' -maskMASK mni_mask.nii' + ssroi_roi_option, False) else: run.command(ssroi_cmd + ' T1.nii T1_preBET' + fsl_suffix + ' -b', False) pre_bet_image = fsl.findImage('T1_preBET') # BET run.command(bet_cmd + ' ' + pre_bet_image + ' T1_BET' + fsl_suffix + ' -f 0.15 -R') fast_t1_input = fsl.findImage('T1_BET' + fsl_suffix) if os.path.exists('T2.nii'): if app.args.nocrop: fast_t2_input = 'T2.nii' else: # Just a reduction of FoV, no sub-voxel interpolation going on run.command('mrtransform T2.nii T2_cropped.nii -template ' + fast_t1_input + ' -interp nearest') fast_t2_input = 'T2_cropped.nii' # Finish branching based on brain masking # FAST if fast_t2_input: run.command(fast_cmd + ' -S 2 ' + fast_t2_input + ' ' + fast_t1_input) else: run.command(fast_cmd + ' ' + fast_t1_input) # FIRST first_input = 'T1.nii' if upsample_for_first: app.warn('Generating 1mm isotropic T1 image for FIRST in hope of preventing failure, since input image is of lower resolution') run.command('mrresize T1.nii T1_1mm.nii -voxel 1.0 -interp sinc') first_input = 'T1_1mm.nii' first_input_brain_extracted_option = '' if app.args.premasked: first_input_brain_extracted_option = ' -b' first_debug_option = '' if not app.cleanup: first_debug_option = ' -d' first_verbosity_option = '' if app.verbosity == 3: first_verbosity_option = ' -v' run.command(first_cmd + ' -m none -s ' + ','.join(sgm_structures) + ' -i ' + first_input + ' -o first' + first_input_brain_extracted_option + first_debug_option + first_verbosity_option) fsl.checkFirst('first', sgm_structures) # Convert FIRST meshes to partial volume images pve_image_list = [ ] progress = app.progressBar('Generating partial volume images for SGM structures', len(sgm_structures)) for struct in sgm_structures: pve_image_path = 'mesh2voxel_' + struct + '.mif' vtk_in_path = 'first-' + struct + '_first.vtk' vtk_temp_path = struct + '.vtk' run.command('meshconvert ' + vtk_in_path + ' ' + vtk_temp_path + ' -transform first2real ' + first_input) run.command('mesh2voxel ' + vtk_temp_path + ' ' + fast_t1_input + ' ' + pve_image_path) pve_image_list.append(pve_image_path) progress.increment() progress.done() run.command('mrmath ' + ' '.join(pve_image_list) + ' sum - | mrcalc - 1.0 -min all_sgms.mif') # Combine the tissue images into the 5TT format within the script itself fast_output_prefix = fast_t1_input.split('.')[0] fast_csf_output = fsl.findImage(fast_output_prefix + '_pve_0') fast_gm_output = fsl.findImage(fast_output_prefix + '_pve_1') fast_wm_output = fsl.findImage(fast_output_prefix + '_pve_2') # Step 1: Run LCC on the WM image run.command('mrthreshold ' + fast_wm_output + ' - -abs 0.001 | maskfilter - connect - -connectivity | mrcalc 1 - 1 -gt -sub remove_unconnected_wm_mask.mif -datatype bit') # Step 2: Generate the images in the same fashion as the old 5ttgen binary used to: # - Preserve CSF as-is # - Preserve SGM, unless it results in a sum of volume fractions greater than 1, in which case clamp # - Multiply the FAST volume fractions of GM and CSF, so that the sum of CSF, SGM, CGM and WM is 1.0 run.command('mrcalc ' + fast_csf_output + ' remove_unconnected_wm_mask.mif -mult csf.mif') run.command('mrcalc 1.0 csf.mif -sub all_sgms.mif -min sgm.mif') run.command('mrcalc 1.0 csf.mif sgm.mif -add -sub ' + fast_gm_output + ' ' + fast_wm_output + ' -add -div multiplier.mif') run.command('mrcalc multiplier.mif -finite multiplier.mif 0.0 -if multiplier_noNAN.mif') run.command('mrcalc ' + fast_gm_output + ' multiplier_noNAN.mif -mult remove_unconnected_wm_mask.mif -mult cgm.mif') run.command('mrcalc ' + fast_wm_output + ' multiplier_noNAN.mif -mult remove_unconnected_wm_mask.mif -mult wm.mif') run.command('mrcalc 0 wm.mif -min path.mif') run.command('mrcat cgm.mif sgm.mif wm.mif csf.mif path.mif - -axis 3 | mrconvert - combined_precrop.mif -strides +2,+3,+4,+1') # Use mrcrop to reduce file size (improves caching of image data during tracking) if app.args.nocrop: run.command('mrconvert combined_precrop.mif result.mif') else: run.command('mrmath combined_precrop.mif sum - -axis 3 | mrthreshold - - -abs 0.5 | mrcrop combined_precrop.mif result.mif -mask -')
def command(cmd, exitOnError=True): import inspect, itertools, os, shlex, subprocess, sys, tempfile from distutils.spawn import find_executable from mrtrix3 import app global _mrtrix_exe_list # Vectorise the command string, preserving anything encased within quotation marks cmdsplit = shlex.split(cmd) if app._lastFile: # Check to see if the last file produced in the previous script execution is # intended to be produced by this command; if it is, this will be the last # command that gets skipped by the -continue option # It's possible that the file might be defined in a '--option=XXX' style argument # It's also possible that the filename in the command string has the file extension omitted for entry in cmdsplit: if entry.startswith('--') and '=' in entry: cmdtotest = entry.split('=')[1] else: cmdtotest = entry filetotest = [ app._lastFile, os.path.splitext(app._lastFile)[0] ] if cmdtotest in filetotest: app.debug('Detected last file \'' + app._lastFile + '\' in command \'' + cmd + '\'; this is the last run.command() / run.function() call that will be skipped') app._lastFile = '' break if app._verbosity: sys.stderr.write(app.colourExec + 'Skipping command:' + app.colourClear + ' ' + cmd + '\n') sys.stderr.flush() return # This splits the command string based on the piping character '|', such that each # individual executable (along with its arguments) appears as its own list # Note that for Python2 support, it is necessary to convert groupby() output from # a generator to a list before it is passed to filter() cmdstack = [ list(g) for k, g in filter(lambda t : t[0], ((k, list(g)) for k, g in itertools.groupby(cmdsplit, lambda s : s is not '|') ) ) ] for line in cmdstack: is_mrtrix_exe = line[0] in _mrtrix_exe_list if is_mrtrix_exe: line[0] = versionMatch(line[0]) if app._nthreads is not None: line.extend( [ '-nthreads', str(app._nthreads) ] ) # Get MRtrix3 binaries to output additional INFO-level information if running in debug mode if app._verbosity == 3: line.append('-info') elif not app._verbosity: line.append('-quiet') else: line[0] = exeName(line[0]) shebang = _shebang(line[0]) if len(shebang): if not is_mrtrix_exe: # If a shebang is found, and this call is therefore invoking an # interpreter, can't rely on the interpreter finding the script # from PATH; need to find the full path ourselves. line[0] = find_executable(line[0]) for item in reversed(shebang): line.insert(0, item) if app._verbosity: sys.stderr.write(app.colourExec + 'Command:' + app.colourClear + ' ' + cmd + '\n') sys.stderr.flush() app.debug('To execute: ' + str(cmdstack)) # Construct temporary text files for holding stdout / stderr contents when appropriate # (One entry per process; each is a tuple containing two entries, each of which is either a # file-like object, or None) tempfiles = [ ] # Execute all processes _processes = [ ] for index, command in enumerate(cmdstack): file_out = None file_err = None # If there's at least one command prior to this, need to receive the stdout from the prior command # at the stdin of this command; otherwise, nothing to receive if index > 0: handle_in = _processes[index-1].stdout else: handle_in = None # If this is not the last command, then stdout needs to be piped to the next command; # otherwise, write stdout to a temporary file so that the contents can be read later if index < len(cmdstack)-1: handle_out = subprocess.PIPE else: file_out = tempfile.TemporaryFile() handle_out = file_out.fileno() # If we're in debug / info mode, the contents of stderr will be read and printed to the terminal # as the command progresses, hence this needs to go to a pipe; otherwise, write it to a temporary # file so that the contents can be read later if app._verbosity > 1: handle_err = subprocess.PIPE else: file_err = tempfile.TemporaryFile() handle_err = file_err.fileno() # Set off the processes try: process = subprocess.Popen (command, stdin=handle_in, stdout=handle_out, stderr=handle_err) _processes.append(process) tempfiles.append( ( file_out, file_err ) ) # FileNotFoundError not defined in Python 2.7 except OSError as e: if exitOnError: app.error('\'' + command[0] + '\' not executed ("' + str(e) + '"); script cannot proceed') else: app.warn('\'' + command[0] + '\' not executed ("' + str(e) + '")') for p in _processes: p.terminate() _processes = [ ] break except (KeyboardInterrupt, SystemExit): import inspect, signal app._handler(signal.SIGINT, inspect.currentframe()) return_stdout = '' return_stderr = '' error = False error_text = '' # Wait for all commands to complete try: # Switch how we monitor running processes / wait for them to complete # depending on whether or not the user has specified -verbose or -debug option if app._verbosity > 1: for process in _processes: stderrdata = '' while True: # Have to read one character at a time: Waiting for a newline character using e.g. readline() will prevent MRtrix progressbars from appearing line = process.stderr.read(1).decode('utf-8') sys.stderr.write(line) sys.stderr.flush() stderrdata += line if not line and process.poll() is not None: break return_stderr += stderrdata if process.returncode: error = True error_text += stderrdata else: for process in _processes: process.wait() except (KeyboardInterrupt, SystemExit): import inspect, signal app._handler(signal.SIGINT, inspect.currentframe()) # For any command stdout / stderr data that wasn't either passed to another command or # printed to the terminal during execution, read it here. for index in range(len(cmdstack)): if tempfiles[index][0] is not None: tempfiles[index][0].flush() tempfiles[index][0].seek(0) stdout_text = tempfiles[index][0].read().decode('utf-8') return_stdout += stdout_text if _processes[index].returncode: error = True error_text += stdout_text if tempfiles[index][1] is not None: tempfiles[index][1].flush() tempfiles[index][1].seek(0) stderr_text = tempfiles[index][1].read().decode('utf-8') return_stderr += stderr_text if _processes[index].returncode: error = True error_text += stderr_text _processes = [ ] if (error): app._cleanup = False if exitOnError: caller = inspect.getframeinfo(inspect.stack()[1][0]) app.console('') sys.stderr.write(os.path.basename(sys.argv[0]) + ': ' + app.colourError + '[ERROR] Command failed: ' + cmd + app.colourClear + app.colourDebug + ' (' + os.path.basename(caller.filename) + ':' + str(caller.lineno) + ')' + app.colourClear + '\n') sys.stderr.write(os.path.basename(sys.argv[0]) + ': ' + app.colourConsole + 'Output of failed command:' + app.colourClear + '\n') sys.stderr.write(error_text) sys.stderr.flush() if app._tempDir: with open(os.path.join(app._tempDir, 'error.txt'), 'w') as outfile: outfile.write(cmd + '\n\n' + error_text + '\n') app.complete() sys.exit(1) else: app.warn('Command failed: ' + cmd) # Only now do we append to the script log, since the command has completed successfully # Note: Writing the command as it was formed as the input to run.command(): # other flags may potentially change if this file is eventually used to resume the script if app._tempDir: with open(os.path.join(app._tempDir, 'log.txt'), 'a') as outfile: outfile.write(cmd + '\n') return (return_stdout, return_stderr)
def execute(): #pylint: disable=unused-variable subject_dir = os.path.abspath(path.from_user(app.ARGS.input, False)) if not os.path.isdir(subject_dir): raise MRtrixError('Input to hsvs algorithm must be a directory') surf_dir = os.path.join(subject_dir, 'surf') mri_dir = os.path.join(subject_dir, 'mri') check_dir(surf_dir) check_dir(mri_dir) #aparc_image = os.path.join(mri_dir, 'aparc+aseg.mgz') aparc_image = 'aparc.mif' mask_image = os.path.join(mri_dir, 'brainmask.mgz') reg_file = os.path.join(mri_dir, 'transforms', 'talairach.xfm') check_file(aparc_image) check_file(mask_image) check_file(reg_file) template_image = 'template.mif' if app.ARGS.template else aparc_image have_first = False have_fast = False fsl_path = os.environ.get('FSLDIR', '') if fsl_path: # Use brain-extracted, bias-corrected image for FSL tools norm_image = os.path.join(mri_dir, 'norm.mgz') check_file(norm_image) run.command('mrconvert ' + norm_image + ' T1.nii -stride -1,+2,+3') # Verify FAST availability try: fast_cmd = fsl.exe_name('fast') except MRtrixError: fast_cmd = None if fast_cmd: have_fast = True if fast_cmd == 'fast': fast_suffix = fsl.suffix() else: fast_suffix = '.nii.gz' else: app.warn('Could not find FSL program fast; script will not use fast for cerebellar tissue segmentation') # Verify FIRST availability try: first_cmd = fsl.exe_name('run_first_all') except MRtrixError: first_cmd = None first_atlas_path = os.path.join(fsl_path, 'data', 'first', 'models_336_bin') have_first = first_cmd and os.path.isdir(first_atlas_path) else: app.warn('Environment variable FSLDIR is not set; script will run without FSL components') acpc_string = 'anterior ' + ('& posterior commissures' if ATTEMPT_PC else 'commissure') have_acpcdetect = bool(find_executable('acpcdetect')) and 'ARTHOME' in os.environ if have_acpcdetect: if have_fast: app.console('ACPCdetect and FSL FAST will be used for explicit segmentation of ' + acpc_string) else: app.warn('ACPCdetect is installed, but FSL FAST not found; cannot segment ' + acpc_string) have_acpcdetect = False else: app.warn('ACPCdetect not installed; cannot segment ' + acpc_string) # Need to perform a better search for hippocampal subfield output: names & version numbers may change have_hipp_subfields = False hipp_subfield_has_amyg = False # Could result in multiple matches hipp_subfield_regex = re.compile(r'^[lr]h\.hippo[a-zA-Z]*Labels-[a-zA-Z0-9]*\.v[0-9]+\.?[a-zA-Z0-9]*\.mg[hz]$') hipp_subfield_all_images = sorted(list(filter(hipp_subfield_regex.match, os.listdir(mri_dir)))) # Remove any images that provide segmentations in FreeSurfer voxel space; we want the high-resolution versions hipp_subfield_all_images = [ item for item in hipp_subfield_all_images if 'FSvoxelSpace' not in item ] # Arrange the images into lr pairs hipp_subfield_paired_images = [ ] for lh_filename in [ item for item in hipp_subfield_all_images if item[0] == 'l' ]: if 'r' + lh_filename[1:] in hipp_subfield_all_images: hipp_subfield_paired_images.append(lh_filename[1:]) # Choose which of these image pairs we are going to use for code in [ '.CA.', '.FS60.' ]: if any(code in filename for filename in hipp_subfield_paired_images): hipp_subfield_image_suffix = [ filename for filename in hipp_subfield_paired_images if code in filename ][0] have_hipp_subfields = True break # Choose the pair with the shortest filename string if we have no other criteria if not have_hipp_subfields and hipp_subfield_paired_images: hipp_subfield_paired_images = sorted(hipp_subfield_paired_images, key=len) if hipp_subfield_paired_images: hipp_subfield_image_suffix = hipp_subfield_paired_images[0] have_hipp_subfields = True if have_hipp_subfields: hipp_subfield_has_amyg = 'Amyg' in hipp_subfield_image_suffix # Perform a similar search for thalamic nuclei submodule output thal_nuclei_image = None thal_nuclei_regex = re.compile(r'^ThalamicNuclei\.v[0-9]+\.?[a-zA-Z0-9]*.mg[hz]$') thal_nuclei_all_images = sorted(list(filter(thal_nuclei_regex.match, os.listdir(mri_dir)))) thal_nuclei_all_images = [ item for item in thal_nuclei_all_images if 'FSvoxelSpace' not in item ] if thal_nuclei_all_images: if len(thal_nuclei_all_images) == 1: thal_nuclei_image = thal_nuclei_all_images[0] else: # How to choose which version to use? # Start with software version thal_nuclei_versions = [ int(item.split('.')[1].lstrip('v')) for item in thal_nuclei_all_images ] thal_nuclei_all_images = [ filepath for filepath, version_number in zip(thal_nuclei_all_images, thal_nuclei_versions) if version_number == max(thal_nuclei_versions) ] if len(thal_nuclei_all_images) == 1: thal_nuclei_image = thal_nuclei_all_images[0] else: # Revert to filename length thal_nuclei_all_images = sorted(thal_nuclei_all_images, key=len) thal_nuclei_image = thal_nuclei_all_images[0] # If particular hippocampal segmentation method is requested, make sure we can perform such; # if not, decide how to segment hippocampus based on what's available hippocampi_method = app.ARGS.hippocampi if hippocampi_method: if hippocampi_method == 'subfields': if not have_hipp_subfields: raise MRtrixError('Could not isolate hippocampal subfields module output (candidate images: ' + str(hipp_subfield_all_images) + ')') elif hippocampi_method == 'first': if not have_first: raise MRtrixError('Cannot use "first" method for hippocampi segmentation; check FSL installation') else: if have_hipp_subfields: hippocampi_method = 'subfields' app.console('Hippocampal subfields module output detected; will utilise for hippocampi ' + ('and amygdalae ' if hipp_subfield_has_amyg else '') + 'segmentation') elif have_first: hippocampi_method = 'first' app.console('No hippocampal subfields module output detected, but FSL FIRST is installed; ' 'will utilise latter for hippocampi segmentation') else: hippocampi_method = 'aseg' app.console('Neither hippocampal subfields module output nor FSL FIRST detected; ' 'FreeSurfer aseg will be used for hippocampi segmentation') if hippocampi_method == 'subfields': if 'FREESURFER_HOME' not in os.environ: raise MRtrixError('FREESURFER_HOME environment variable not set; required for use of hippocampal subfields module') freesurfer_lut_file = os.path.join(os.environ['FREESURFER_HOME'], 'FreeSurferColorLUT.txt') check_file(freesurfer_lut_file) hipp_lut_file = os.path.join(path.shared_data_path(), path.script_subdir_name(), 'hsvs', 'HippSubfields.txt') check_file(hipp_lut_file) if hipp_subfield_has_amyg: amyg_lut_file = os.path.join(path.shared_data_path(), path.script_subdir_name(), 'hsvs', 'AmygSubfields.txt') check_file(amyg_lut_file) if app.ARGS.sgm_amyg_hipp: app.warn('Option -sgm_amyg_hipp ignored ' '(hsvs algorithm always assigns hippocampi & ampygdalae as sub-cortical grey matter)') # Similar logic for thalami thalami_method = app.ARGS.thalami if thalami_method: if thalami_method == 'nuclei': if not thal_nuclei_image: raise MRtrixError('Could not find thalamic nuclei module output') elif thalami_method == 'first': if not have_first: raise MRtrixError('Cannot use "first" method for thalami segmentation; check FSL installation') else: # Not happy with outputs of thalamic nuclei submodule; default to FIRST if have_first: thalami_method = 'first' if thal_nuclei_image: app.console('Thalamic nuclei submodule output ignored in favour of FSL FIRST ' '(can override using -thalami option)') else: app.console('Will utilise FSL FIRST for thalami segmentation') elif thal_nuclei_image: thalami_method = 'nuclei' app.console('Will utilise detected thalamic nuclei submodule output') else: thalami_method = 'aseg' app.console('Neither thalamic nuclei module output nor FSL FIRST detected; ' 'FreeSurfer aseg will be used for thalami segmentation') ########################### # Commencing segmentation # ########################### tissue_images = [ [ 'lh.pial.mif', 'rh.pial.mif' ], [], [ 'lh.white.mif', 'rh.white.mif' ], [], [] ] # Get the main cerebrum segments; these are already smooth progress = app.ProgressBar('Mapping FreeSurfer cortical reconstruction to partial volume images', 8) for hemi in [ 'lh', 'rh' ]: for basename in [ hemi+'.white', hemi+'.pial' ]: filepath = os.path.join(surf_dir, basename) check_file(filepath) transformed_path = basename + '_realspace.obj' run.command('meshconvert ' + filepath + ' ' + transformed_path + ' -binary -transform fs2real ' + aparc_image) progress.increment() run.command('mesh2voxel ' + transformed_path + ' ' + template_image + ' ' + basename + '.mif') app.cleanup(transformed_path) progress.increment() progress.done() # Get other structures that need to be converted from the aseg voxel image from_aseg = list(ASEG_STRUCTURES) if hippocampi_method == 'subfields': if not hipp_subfield_has_amyg and not have_first: from_aseg.extend(AMYG_ASEG) elif hippocampi_method == 'aseg': from_aseg.extend(HIPP_ASEG) from_aseg.extend(AMYG_ASEG) if thalami_method == 'aseg': from_aseg.extend(THAL_ASEG) if not have_first: from_aseg.extend(OTHER_SGM_ASEG) progress = app.ProgressBar('Smoothing non-cortical structures segmented by FreeSurfer', len(from_aseg) + 2) for (index, tissue, name) in from_aseg: init_mesh_path = name + '_init.vtk' smoothed_mesh_path = name + '.vtk' run.command('mrcalc ' + aparc_image + ' ' + str(index) + ' -eq - | voxel2mesh - -threshold 0.5 ' + init_mesh_path) run.command('meshfilter ' + init_mesh_path + ' smooth ' + smoothed_mesh_path) app.cleanup(init_mesh_path) run.command('mesh2voxel ' + smoothed_mesh_path + ' ' + template_image + ' ' + name + '.mif') app.cleanup(smoothed_mesh_path) tissue_images[tissue-1].append(name + '.mif') progress.increment() # Lateral ventricles are separate as we want to combine with choroid plexus prior to mesh conversion for hemi_index, hemi_name in enumerate(['Left', 'Right']): name = hemi_name + '_LatVent_ChorPlex' init_mesh_path = name + '_init.vtk' smoothed_mesh_path = name + '.vtk' run.command('mrcalc ' + ' '.join(aparc_image + ' ' + str(index) + ' -eq' for index, tissue, name in VENTRICLE_CP_ASEG[hemi_index]) + ' -add - | ' + 'voxel2mesh - -threshold 0.5 ' + init_mesh_path) run.command('meshfilter ' + init_mesh_path + ' smooth ' + smoothed_mesh_path) app.cleanup(init_mesh_path) run.command('mesh2voxel ' + smoothed_mesh_path + ' ' + template_image + ' ' + name + '.mif') app.cleanup(smoothed_mesh_path) tissue_images[3].append(name + '.mif') progress.increment() progress.done() # Combine corpus callosum segments before smoothing progress = app.ProgressBar('Combining and smoothing corpus callosum segmentation', len(CORPUS_CALLOSUM_ASEG) + 3) for (index, name) in CORPUS_CALLOSUM_ASEG: run.command('mrcalc ' + aparc_image + ' ' + str(index) + ' -eq ' + name + '.mif -datatype bit') progress.increment() cc_init_mesh_path = 'combined_corpus_callosum_init.vtk' cc_smoothed_mesh_path = 'combined_corpus_callosum.vtk' run.command('mrmath ' + ' '.join([ name + '.mif' for (index, name) in CORPUS_CALLOSUM_ASEG ]) + ' sum - | voxel2mesh - -threshold 0.5 ' + cc_init_mesh_path) for name in [ n for _, n in CORPUS_CALLOSUM_ASEG ]: app.cleanup(name + '.mif') progress.increment() run.command('meshfilter ' + cc_init_mesh_path + ' smooth ' + cc_smoothed_mesh_path) app.cleanup(cc_init_mesh_path) progress.increment() run.command('mesh2voxel ' + cc_smoothed_mesh_path + ' ' + template_image + ' combined_corpus_callosum.mif') app.cleanup(cc_smoothed_mesh_path) progress.done() tissue_images[2].append('combined_corpus_callosum.mif') # Deal with brain stem, including determining those voxels that should # be erased from the 5TT image in order for streamlines traversing down # the spinal column to be terminated & accepted bs_fullmask_path = 'brain_stem_init.mif' bs_cropmask_path = '' progress = app.ProgressBar('Segmenting and cropping brain stem', 5) run.command('mrcalc ' + aparc_image + ' ' + str(BRAIN_STEM_ASEG[0][0]) + ' -eq ' + ' -add '.join([ aparc_image + ' ' + str(index) + ' -eq' for index, name in BRAIN_STEM_ASEG[1:] ]) + ' -add ' + bs_fullmask_path + ' -datatype bit') progress.increment() bs_init_mesh_path = 'brain_stem_init.vtk' run.command('voxel2mesh ' + bs_fullmask_path + ' ' + bs_init_mesh_path) progress.increment() bs_smoothed_mesh_path = 'brain_stem.vtk' run.command('meshfilter ' + bs_init_mesh_path + ' smooth ' + bs_smoothed_mesh_path) app.cleanup(bs_init_mesh_path) progress.increment() run.command('mesh2voxel ' + bs_smoothed_mesh_path + ' ' + template_image + ' brain_stem.mif') app.cleanup(bs_smoothed_mesh_path) progress.increment() fourthventricle_zmin = min([ int(line.split()[2]) for line in run.command('maskdump 4th-Ventricle.mif')[0].splitlines() ]) if fourthventricle_zmin: bs_cropmask_path = 'brain_stem_crop.mif' run.command('mredit brain_stem.mif - ' + ' '.join([ '-plane 2 ' + str(index) + ' 0' for index in range(0, fourthventricle_zmin) ]) + ' | ' 'mrcalc brain_stem.mif - -sub 1e-6 -gt ' + bs_cropmask_path + ' -datatype bit') app.cleanup(bs_fullmask_path) progress.done() if hippocampi_method == 'subfields': progress = app.ProgressBar('Using detected FreeSurfer hippocampal subfields module output', 64 if hipp_subfield_has_amyg else 32) subfields = [ ( hipp_lut_file, 'hipp' ) ] if hipp_subfield_has_amyg: subfields.append(( amyg_lut_file, 'amyg' )) for subfields_lut_file, structure_name in subfields: for hemi, filename in zip([ 'Left', 'Right'], [ prefix + hipp_subfield_image_suffix for prefix in [ 'l', 'r' ] ]): # Extract individual components from image and assign to different tissues subfields_all_tissues_image = hemi + '_' + structure_name + '_subfields.mif' run.command('labelconvert ' + os.path.join(mri_dir, filename) + ' ' + freesurfer_lut_file + ' ' + subfields_lut_file + ' ' + subfields_all_tissues_image) progress.increment() for tissue in range(0, 5): init_mesh_path = hemi + '_' + structure_name + '_subfield_' + str(tissue) + '_init.vtk' smooth_mesh_path = hemi + '_' + structure_name + '_subfield_' + str(tissue) + '.vtk' subfield_tissue_image = hemi + '_' + structure_name + '_subfield_' + str(tissue) + '.mif' run.command('mrcalc ' + subfields_all_tissues_image + ' ' + str(tissue+1) + ' -eq - | ' + \ 'voxel2mesh - ' + init_mesh_path) progress.increment() # Since the hippocampal subfields segmentation can include some fine structures, reduce the extent of smoothing run.command('meshfilter ' + init_mesh_path + ' smooth ' + smooth_mesh_path + ' -smooth_spatial 2 -smooth_influence 2') app.cleanup(init_mesh_path) progress.increment() run.command('mesh2voxel ' + smooth_mesh_path + ' ' + template_image + ' ' + subfield_tissue_image) app.cleanup(smooth_mesh_path) progress.increment() tissue_images[tissue].append(subfield_tissue_image) app.cleanup(subfields_all_tissues_image) progress.done() if thalami_method == 'nuclei': progress = app.ProgressBar('Using detected FreeSurfer thalamic nuclei module output', 6) for hemi in ['Left', 'Right']: thal_mask_path = hemi + '_Thalamus_mask.mif' init_mesh_path = hemi + '_Thalamus_init.vtk' smooth_mesh_path = hemi + '_Thalamus.vtk' thalamus_image = hemi + '_Thalamus.mif' if hemi == 'Right': run.command('mrthreshold ' + os.path.join(mri_dir, thal_nuclei_image) + ' -abs 8200 ' + thal_mask_path) else: run.command('mrcalc ' + os.path.join(mri_dir, thal_nuclei_image) + ' 0 -gt ' + os.path.join(mri_dir, thal_nuclei_image) + ' 8200 -lt ' + '-mult ' + thal_mask_path) run.command('voxel2mesh ' + thal_mask_path + ' ' + init_mesh_path) app.cleanup(thal_mask_path) progress.increment() run.command('meshfilter ' + init_mesh_path + ' smooth ' + smooth_mesh_path + ' -smooth_spatial 2 -smooth_influence 2') app.cleanup(init_mesh_path) progress.increment() run.command('mesh2voxel ' + smooth_mesh_path + ' ' + template_image + ' ' + thalamus_image) app.cleanup(smooth_mesh_path) progress.increment() tissue_images[1].append(thalamus_image) progress.done() if have_first: app.console('Running FSL FIRST to segment sub-cortical grey matter structures') from_first = SGM_FIRST_MAP.copy() if hippocampi_method == 'subfields': from_first = { key: value for key, value in from_first.items() if 'Hippocampus' not in value } if hipp_subfield_has_amyg: from_first = { key: value for key, value in from_first.items() if 'Amygdala' not in value } elif hippocampi_method == 'aseg': from_first = { key: value for key, value in from_first.items() if 'Hippocampus' not in value and 'Amygdala' not in value } if thalami_method != 'first': from_first = { key: value for key, value in from_first.items() if 'Thalamus' not in value } run.command(first_cmd + ' -s ' + ','.join(from_first.keys()) + ' -i T1.nii -b -o first') fsl.check_first('first', from_first.keys()) app.cleanup(glob.glob('T1_to_std_sub.*')) progress = app.ProgressBar('Mapping FIRST segmentations to image', 2*len(from_first)) for key, value in from_first.items(): vtk_in_path = 'first-' + key + '_first.vtk' vtk_converted_path = 'first-' + key + '_transformed.vtk' run.command('meshconvert ' + vtk_in_path + ' ' + vtk_converted_path + ' -transform first2real T1.nii') app.cleanup(vtk_in_path) progress.increment() run.command('mesh2voxel ' + vtk_converted_path + ' ' + template_image + ' ' + value + '.mif') app.cleanup(vtk_converted_path) tissue_images[1].append(value + '.mif') progress.increment() if not have_fast: app.cleanup('T1.nii') app.cleanup(glob.glob('first*')) progress.done() # Run ACPCdetect, use results to draw spherical ROIs on T1 that will be fed to FSL FAST, # the WM components of which will then be added to the 5TT if have_acpcdetect: progress = app.ProgressBar('Using ACPCdetect and FAST to segment ' + acpc_string, 5) # ACPCdetect requires input image to be 16-bit # We also want to realign to RAS beforehand so that we can interpret the output voxel locations properly acpcdetect_input_image = 'T1RAS_16b.nii' run.command('mrconvert ' + norm_image + ' -datatype uint16 -stride +1,+2,+3 ' + acpcdetect_input_image) progress.increment() run.command('acpcdetect -i ' + acpcdetect_input_image) progress.increment() # We need the header in order to go from voxel coordinates to scanner coordinates acpcdetect_input_header = image.Header(acpcdetect_input_image) acpcdetect_output_path = os.path.splitext(acpcdetect_input_image)[0] + '_ACPC.txt' app.cleanup(acpcdetect_input_image) with open(acpcdetect_output_path, 'r') as acpc_file: acpcdetect_output_data = acpc_file.read().splitlines() app.cleanup(glob.glob(os.path.splitext(acpcdetect_input_image)[0] + "*")) # Need to scan through the contents of this file, # isolating the AC and PC locations ac_voxel = pc_voxel = None for index, line in enumerate(acpcdetect_output_data): if 'AC' in line and 'voxel location' in line: ac_voxel = [float(item) for item in acpcdetect_output_data[index+1].strip().split()] elif 'PC' in line and 'voxel location' in line: pc_voxel = [float(item) for item in acpcdetect_output_data[index+1].strip().split()] if not ac_voxel or not pc_voxel: raise MRtrixError('Error parsing text file from "acpcdetect"') def voxel2scanner(voxel, header): return [ voxel[0]*header.spacing()[0]*header.transform()[axis][0] + voxel[1]*header.spacing()[1]*header.transform()[axis][1] + voxel[2]*header.spacing()[2]*header.transform()[axis][2] + header.transform()[axis][3] for axis in range(0,3) ] ac_scanner = voxel2scanner(ac_voxel, acpcdetect_input_header) pc_scanner = voxel2scanner(pc_voxel, acpcdetect_input_header) # Generate the mask image within which FAST will be run acpc_prefix = 'ACPC' if ATTEMPT_PC else 'AC' acpc_mask_image = acpc_prefix + '_FAST_mask.mif' run.command('mrcalc ' + template_image + ' nan -eq - | ' 'mredit - ' + acpc_mask_image + ' -scanner ' '-sphere ' + ','.join(str(value) for value in ac_scanner) + ' 8 1 ' + ('-sphere ' + ','.join(str(value) for value in pc_scanner) + ' 5 1' if ATTEMPT_PC else '')) progress.increment() acpc_t1_masked_image = acpc_prefix + '_T1.nii' run.command('mrtransform ' + norm_image + ' -template ' + template_image + ' - | ' 'mrcalc - ' + acpc_mask_image + ' -mult ' + acpc_t1_masked_image) app.cleanup(acpc_mask_image) progress.increment() run.command(fast_cmd + ' -N ' + acpc_t1_masked_image) app.cleanup(acpc_t1_masked_image) progress.increment() # Ideally don't want to have to add these manually; instead add all outputs from FAST # to the 5TT (both cerebellum and AC / PC) in a single go # This should involve grabbing just the WM component of these images # Actually, in retrospect, it may be preferable to do the AC PC segmentation # earlier on, and simply add them to the list of WM structures acpc_wm_image = acpc_prefix + '.mif' run.command('mrconvert ' + fsl.find_image(acpc_prefix + '_T1_pve_2') + ' ' + acpc_wm_image) tissue_images[2].append(acpc_wm_image) app.cleanup(glob.glob(os.path.splitext(acpc_t1_masked_image)[0] + '*')) progress.done() # If we don't have FAST, do cerebellar segmentation in a comparable way to the cortical GM / WM: # Generate one 'pial-like' surface containing the GM and WM of the cerebellum, # and another with just the WM if not have_fast: progress = app.ProgressBar('Adding FreeSurfer cerebellar segmentations directly', 6) for hemi in [ 'Left-', 'Right-' ]: wm_index = [ index for index, tissue, name in CEREBELLUM_ASEG if name.startswith(hemi) and 'White' in name ][0] gm_index = [ index for index, tissue, name in CEREBELLUM_ASEG if name.startswith(hemi) and 'Cortex' in name ][0] run.command('mrcalc ' + aparc_image + ' ' + str(wm_index) + ' -eq ' + aparc_image + ' ' + str(gm_index) + ' -eq -add - | ' + \ 'voxel2mesh - ' + hemi + 'cerebellum_all_init.vtk') progress.increment() run.command('mrcalc ' + aparc_image + ' ' + str(gm_index) + ' -eq - | ' + \ 'voxel2mesh - ' + hemi + 'cerebellum_grey_init.vtk') progress.increment() for name, tissue in { 'all':2, 'grey':1 }.items(): run.command('meshfilter ' + hemi + 'cerebellum_' + name + '_init.vtk smooth ' + hemi + 'cerebellum_' + name + '.vtk') app.cleanup(hemi + 'cerebellum_' + name + '_init.vtk') progress.increment() run.command('mesh2voxel ' + hemi + 'cerebellum_' + name + '.vtk ' + template_image + ' ' + hemi + 'cerebellum_' + name + '.mif') app.cleanup(hemi + 'cerebellum_' + name + '.vtk') progress.increment() tissue_images[tissue].append(hemi + 'cerebellum_' + name + '.mif') progress.done() # Construct images with the partial volume of each tissue progress = app.ProgressBar('Combining segmentations of all structures corresponding to each tissue type', 5) for tissue in range(0,5): run.command('mrmath ' + ' '.join(tissue_images[tissue]) + (' brain_stem.mif' if tissue == 2 else '') + ' sum - | mrcalc - 1.0 -min tissue' + str(tissue) + '_init.mif') app.cleanup(tissue_images[tissue]) progress.increment() progress.done() # This can hopefully be done with a connected-component analysis: Take just the WM image, and # fill in any gaps (i.e. select the inverse, select the largest connected component, invert again) # Make sure that floating-point values are handled appropriately # Combine these images together using the appropriate logic in order to form the 5TT image progress = app.ProgressBar('Modulating segmentation images based on other tissues', 9) tissue_images = [ 'tissue0.mif', 'tissue1.mif', 'tissue2.mif', 'tissue3.mif', 'tissue4.mif' ] run.function(os.rename, 'tissue4_init.mif', 'tissue4.mif') progress.increment() run.command('mrcalc tissue3_init.mif tissue3_init.mif ' + tissue_images[4] + ' -add 1.0 -sub 0.0 -max -sub 0.0 -max ' + tissue_images[3]) app.cleanup('tissue3_init.mif') progress.increment() run.command('mrmath ' + ' '.join(tissue_images[3:5]) + ' sum tissuesum_34.mif') progress.increment() run.command('mrcalc tissue1_init.mif tissue1_init.mif tissuesum_34.mif -add 1.0 -sub 0.0 -max -sub 0.0 -max ' + tissue_images[1]) app.cleanup('tissue1_init.mif') app.cleanup('tissuesum_34.mif') progress.increment() run.command('mrmath ' + tissue_images[1] + ' ' + ' '.join(tissue_images[3:5]) + ' sum tissuesum_134.mif') progress.increment() run.command('mrcalc tissue2_init.mif tissue2_init.mif tissuesum_134.mif -add 1.0 -sub 0.0 -max -sub 0.0 -max ' + tissue_images[2]) app.cleanup('tissue2_init.mif') app.cleanup('tissuesum_134.mif') progress.increment() run.command('mrmath ' + ' '.join(tissue_images[1:5]) + ' sum tissuesum_1234.mif') progress.increment() run.command('mrcalc tissue0_init.mif tissue0_init.mif tissuesum_1234.mif -add 1.0 -sub 0.0 -max -sub 0.0 -max ' + tissue_images[0]) app.cleanup('tissue0_init.mif') app.cleanup('tissuesum_1234.mif') progress.increment() tissue_sum_image = 'tissuesum_01234.mif' run.command('mrmath ' + ' '.join(tissue_images) + ' sum ' + tissue_sum_image) progress.done() if app.ARGS.template: run.command('mrtransform ' + mask_image + ' -template template.mif - | mrthreshold - brainmask.mif -abs 0.5') mask_image = 'brainmask.mif' # Branch depending on whether or not FSL fast will be used to re-segment the cerebellum if have_fast: # How to support -template option? # - Re-grid norm.mgz to template image before running FAST # - Re-grid FAST output to template image # Consider splitting, including initial mapping of cerebellar regions: # - If we're not using a separate template image, just map cerebellar regions to voxels to # produce a mask, and run FAST within that mask # - If we have a template, combine cerebellar regions, convert to surfaces (one per hemisphere), # map these to the template image, run FIRST on a binary mask from this, then # re-combine this with the tissue maps from other sources based on the estimated PVF of # cerebellum meshes cerebellum_volume_image = 'Cerebellum_volume.mif' cerebellum_mask_image = 'Cerebellum_mask.mif' t1_cerebellum_masked = 'T1_cerebellum_precrop.mif' if app.ARGS.template: # If this is the case, then we haven't yet performed any cerebellar segmentation / meshing # What we want to do is: for each hemisphere, combine all three "cerebellar" segments from FreeSurfer, # convert to a surface, map that surface to the template image progress = app.ProgressBar('Preparing images of cerebellum for intensity-based segmentation', 9) cerebellar_hemi_pvf_images = [ ] for hemi in [ 'Left', 'Right' ]: init_mesh_path = hemi + '-Cerebellum-All-Init.vtk' smooth_mesh_path = hemi + '-Cerebellum-All-Smooth.vtk' pvf_image_path = hemi + '-Cerebellum-PVF-Template.mif' cerebellum_aseg_hemi = [ entry for entry in CEREBELLUM_ASEG if hemi in entry[2] ] run.command('mrcalc ' + aparc_image + ' ' + str(cerebellum_aseg_hemi[0][0]) + ' -eq ' + \ ' -add '.join([ aparc_image + ' ' + str(index) + ' -eq' for index, tissue, name in cerebellum_aseg_hemi[1:] ]) + ' -add - | ' + \ 'voxel2mesh - ' + init_mesh_path) progress.increment() run.command('meshfilter ' + init_mesh_path + ' smooth ' + smooth_mesh_path) app.cleanup(init_mesh_path) progress.increment() run.command('mesh2voxel ' + smooth_mesh_path + ' ' + template_image + ' ' + pvf_image_path) app.cleanup(smooth_mesh_path) cerebellar_hemi_pvf_images.append(pvf_image_path) progress.increment() # Combine the two hemispheres together into: # - An image in preparation for running FAST # - A combined total partial volume fraction image that will be later used for tissue recombination run.command('mrcalc ' + ' '.join(cerebellar_hemi_pvf_images) + ' -add 1.0 -min ' + cerebellum_volume_image) app.cleanup(cerebellar_hemi_pvf_images) progress.increment() run.command('mrthreshold ' + cerebellum_volume_image + ' ' + cerebellum_mask_image + ' -abs 1e-6') progress.increment() run.command('mrtransform ' + norm_image + ' -template ' + template_image + ' - | ' + \ 'mrcalc - ' + cerebellum_mask_image + ' -mult ' + t1_cerebellum_masked) progress.done() else: app.console('Preparing images of cerebellum for intensity-based segmentation') run.command('mrcalc ' + aparc_image + ' ' + str(CEREBELLUM_ASEG[0][0]) + ' -eq ' + \ ' -add '.join([ aparc_image + ' ' + str(index) + ' -eq' for index, tissue, name in CEREBELLUM_ASEG[1:] ]) + ' -add ' + \ cerebellum_volume_image) cerebellum_mask_image = cerebellum_volume_image run.command('mrcalc T1.nii ' + cerebellum_mask_image + ' -mult ' + t1_cerebellum_masked) app.cleanup('T1.nii') # Any code below here should be compatible with cerebellum_volume_image.mif containing partial volume fractions # (in the case of no explicit template image, it's a mask, but the logic still applies) app.console('Running FSL fast to segment the cerebellum based on intensity information') # Run FSL FAST just within the cerebellum # FAST memory usage can also be huge when using a high-resolution template image: # Crop T1 image around the cerebellum before feeding to FAST, then re-sample to full template image FoV fast_input_image = 'T1_cerebellum.nii' run.command('mrgrid ' + t1_cerebellum_masked + ' crop -mask ' + cerebellum_mask_image + ' ' + fast_input_image) app.cleanup(t1_cerebellum_masked) # Cleanup of cerebellum_mask_image: # May be same image as cerebellum_volume_image, which is required later if cerebellum_mask_image != cerebellum_volume_image: app.cleanup(cerebellum_mask_image) run.command(fast_cmd + ' -N ' + fast_input_image) app.cleanup(fast_input_image) # Use glob to clean up unwanted FAST outputs fast_output_prefix = os.path.splitext(fast_input_image)[0] fast_pve_output_prefix = fast_output_prefix + '_pve_' app.cleanup([ entry for entry in glob.glob(fast_output_prefix + '*') if not fast_pve_output_prefix in entry ]) progress = app.ProgressBar('Introducing intensity-based cerebellar segmentation into the 5TT image', 10) fast_outputs_cropped = [ fast_pve_output_prefix + str(n) + fast_suffix for n in range(0,3) ] fast_outputs_template = [ 'FAST_' + str(n) + '.mif' for n in range(0,3) ] for inpath, outpath in zip(fast_outputs_cropped, fast_outputs_template): run.command('mrtransform ' + inpath + ' -interp nearest -template ' + template_image + ' ' + outpath) app.cleanup(inpath) progress.increment() if app.ARGS.template: app.cleanup(template_image) # Generate the revised tissue images, using output from FAST inside the cerebellum and # output from previous processing everywhere else # Note that the middle intensity (grey matter) in the FAST output here gets assigned # to the sub-cortical grey matter component # Some of these voxels may have existing non-zero tissue components. # In that case, let's find a multiplier to apply to cerebellum tissues such that the # sum does not exceed 1.0 new_tissue_images = [ 'tissue0_fast.mif', 'tissue1_fast.mif', 'tissue2_fast.mif', 'tissue3_fast.mif', 'tissue4_fast.mif' ] new_tissue_sum_image = 'tissuesum_01234_fast.mif' cerebellum_multiplier_image = 'Cerebellar_multiplier.mif' run.command('mrcalc ' + cerebellum_volume_image + ' ' + tissue_sum_image + ' -add 0.5 -gt 1.0 ' + tissue_sum_image + ' -sub 0.0 -if ' + cerebellum_multiplier_image) app.cleanup(cerebellum_volume_image) progress.increment() run.command('mrconvert ' + tissue_images[0] + ' ' + new_tissue_images[0]) app.cleanup(tissue_images[0]) progress.increment() run.command('mrcalc ' + tissue_images[1] + ' ' + cerebellum_multiplier_image + ' ' + fast_outputs_template[1] + ' -mult -add ' + new_tissue_images[1]) app.cleanup(tissue_images[1]) app.cleanup(fast_outputs_template[1]) progress.increment() run.command('mrcalc ' + tissue_images[2] + ' ' + cerebellum_multiplier_image + ' ' + fast_outputs_template[2] + ' -mult -add ' + new_tissue_images[2]) app.cleanup(tissue_images[2]) app.cleanup(fast_outputs_template[2]) progress.increment() run.command('mrcalc ' + tissue_images[3] + ' ' + cerebellum_multiplier_image + ' ' + fast_outputs_template[0] + ' -mult -add ' + new_tissue_images[3]) app.cleanup(tissue_images[3]) app.cleanup(fast_outputs_template[0]) app.cleanup(cerebellum_multiplier_image) progress.increment() run.command('mrconvert ' + tissue_images[4] + ' ' + new_tissue_images[4]) app.cleanup(tissue_images[4]) progress.increment() run.command('mrmath ' + ' '.join(new_tissue_images) + ' sum ' + new_tissue_sum_image) app.cleanup(tissue_sum_image) progress.done() tissue_images = new_tissue_images tissue_sum_image = new_tissue_sum_image # For all voxels within FreeSurfer's brain mask, add to the CSF image in order to make the sum 1.0 progress = app.ProgressBar('Performing fill operations to preserve unity tissue volume', 2) # Some voxels may get a non-zero cortical GM fraction due to native use of the surface representation, yet # these voxels are actually outside FreeSurfer's own provided brain mask. So what we need to do here is # get the union of the tissue sum nonzero image and the mask image, and use that at the -mult step of the # mrcalc call. # Required image: (tissue_sum_image > 0.0) || mask_image # tissue_sum_image 0.0 -gt mask_image -add 1.0 -min new_tissue_images = [ tissue_images[0], tissue_images[1], tissue_images[2], os.path.splitext(tissue_images[3])[0] + '_filled.mif', tissue_images[4] ] csf_fill_image = 'csf_fill.mif' run.command('mrcalc 1.0 ' + tissue_sum_image + ' -sub ' + tissue_sum_image + ' 0.0 -gt ' + mask_image + ' -add 1.0 -min -mult 0.0 -max ' + csf_fill_image) app.cleanup(tissue_sum_image) # If no template is specified, this file is part of the FreeSurfer output; hence don't modify if app.ARGS.template: app.cleanup(mask_image) progress.increment() run.command('mrcalc ' + tissue_images[3] + ' ' + csf_fill_image + ' -add ' + new_tissue_images[3]) app.cleanup(csf_fill_image) app.cleanup(tissue_images[3]) progress.done() tissue_images = new_tissue_images # Move brain stem from white matter to pathology at final step: # this prevents the brain stem segmentation from overwriting other # structures that it otherwise wouldn't if it were written to WM if not app.ARGS.white_stem: progress = app.ProgressBar('Moving brain stem to volume index 4', 3) new_tissue_images = [ tissue_images[0], tissue_images[1], os.path.splitext(tissue_images[2])[0] + '_no_brainstem.mif', tissue_images[3], os.path.splitext(tissue_images[4])[0] + '_with_brainstem.mif' ] run.command('mrcalc ' + tissue_images[2] + ' brain_stem.mif -min brain_stem_white_overlap.mif') app.cleanup('brain_stem.mif') progress.increment() run.command('mrcalc ' + tissue_images[2] + ' brain_stem_white_overlap.mif -sub ' + new_tissue_images[2]) app.cleanup(tissue_images[2]) progress.increment() run.command('mrcalc ' + tissue_images[4] + ' brain_stem_white_overlap.mif -add ' + new_tissue_images[4]) app.cleanup(tissue_images[4]) app.cleanup('brain_stem_white_overlap.mif') progress.done() tissue_images = new_tissue_images # Finally, concatenate the volumes to produce the 5TT image app.console('Concatenating tissue volumes into 5TT format') precrop_result_image = '5TT.mif' if bs_cropmask_path: run.command('mrcat ' + ' '.join(tissue_images) + ' - -axis 3 | ' + \ '5ttedit - ' + precrop_result_image + ' -none ' + bs_cropmask_path) app.cleanup(bs_cropmask_path) else: run.command('mrcat ' + ' '.join(tissue_images) + ' ' + precrop_result_image + ' -axis 3') app.cleanup(tissue_images) # Maybe don't go off all tissues here, since FreeSurfer's mask can be fairly liberal; # instead get just a voxel clearance from all other tissue types (maybe two) if app.ARGS.nocrop: run.function(os.rename, precrop_result_image, 'result.mif') else: app.console('Cropping final 5TT image') crop_mask_image = 'crop_mask.mif' run.command('mrconvert ' + precrop_result_image + ' -coord 3 0,1,2,4 - | mrmath - sum - -axis 3 | mrthreshold - - -abs 0.001 | maskfilter - dilate ' + crop_mask_image) run.command('mrgrid ' + precrop_result_image + ' crop result.mif -mask ' + crop_mask_image) app.cleanup(crop_mask_image) app.cleanup(precrop_result_image) run.command('mrconvert result.mif ' + path.from_user(app.ARGS.output), mrconvert_keyval=path.from_user(os.path.join(app.ARGS.input, 'mri', 'aparc+aseg.mgz'), True), force=app.FORCE_OVERWRITE)
def command(cmd, exitOnError=True): #pylint: disable=unused-variable import inspect, itertools, shlex, signal, string, subprocess, sys, tempfile from distutils.spawn import find_executable from mrtrix3 import app # This is the only global variable that is _modified_ within this function global _processes # Vectorise the command string, preserving anything encased within quotation marks if os.sep == '/': # Cheap POSIX compliance check cmdsplit = shlex.split(cmd) else: # Native Windows Python cmdsplit = [ entry.strip('\"') for entry in shlex.split(cmd, posix=False) ] if _lastFile: if _triggerContinue(cmdsplit): app.debug('Detected last file in command \'' + cmd + '\'; this is the last run.command() / run.function() call that will be skipped') if app.verbosity: sys.stderr.write(app.colourExec + 'Skipping command:' + app.colourClear + ' ' + cmd + '\n') sys.stderr.flush() return ('', '') # This splits the command string based on the piping character '|', such that each # individual executable (along with its arguments) appears as its own list cmdstack = [ list(g) for k, g in itertools.groupby(cmdsplit, lambda s : s != '|') if k ] for line in cmdstack: is_mrtrix_exe = line[0] in _mrtrix_exe_list if is_mrtrix_exe: line[0] = versionMatch(line[0]) if app.numThreads is not None: line.extend( [ '-nthreads', str(app.numThreads) ] ) # Get MRtrix3 binaries to output additional INFO-level information if running in debug mode if app.verbosity == 3: line.append('-info') elif not app.verbosity: line.append('-quiet') else: line[0] = exeName(line[0]) shebang = _shebang(line[0]) if shebang: if not is_mrtrix_exe: # If a shebang is found, and this call is therefore invoking an # interpreter, can't rely on the interpreter finding the script # from PATH; need to find the full path ourselves. line[0] = find_executable(line[0]) for item in reversed(shebang): line.insert(0, item) app.debug('To execute: ' + str(cmdstack)) if app.verbosity: sys.stderr.write(app.colourExec + 'Command:' + app.colourClear + ' ' + cmd + '\n') sys.stderr.flush() # Disable interrupt signal handler while threads are running try: signal.signal(signal.SIGINT, signal.default_int_handler) except: pass # Construct temporary text files for holding stdout / stderr contents when appropriate # (One entry per process; each is a tuple containing two entries, each of which is either a # file-like object, or None) tempfiles = [ ] # Execute all processes assert not _processes for index, to_execute in enumerate(cmdstack): file_out = None file_err = None # If there's at least one command prior to this, need to receive the stdout from the prior command # at the stdin of this command; otherwise, nothing to receive if index > 0: handle_in = _processes[index-1].stdout else: handle_in = None # If this is not the last command, then stdout needs to be piped to the next command; # otherwise, write stdout to a temporary file so that the contents can be read later if index < len(cmdstack)-1: handle_out = subprocess.PIPE else: file_out = tempfile.TemporaryFile() handle_out = file_out.fileno() # If we're in debug / info mode, the contents of stderr will be read and printed to the terminal # as the command progresses, hence this needs to go to a pipe; otherwise, write it to a temporary # file so that the contents can be read later if app.verbosity > 1: handle_err = subprocess.PIPE else: file_err = tempfile.TemporaryFile() handle_err = file_err.fileno() # Set off the processes try: try: process = subprocess.Popen (to_execute, stdin=handle_in, stdout=handle_out, stderr=handle_err, env=_env, preexec_fn=os.setpgrp) # pylint: disable=bad-option-value,subprocess-popen-preexec-fn except AttributeError: process = subprocess.Popen (to_execute, stdin=handle_in, stdout=handle_out, stderr=handle_err, env=_env) _processes.append(process) tempfiles.append( ( file_out, file_err ) ) # FileNotFoundError not defined in Python 2.7 except OSError as e: if exitOnError: app.error('\'' + to_execute[0] + '\' not executed ("' + str(e) + '"); script cannot proceed') else: app.warn('\'' + to_execute[0] + '\' not executed ("' + str(e) + '")') for p in _processes: p.terminate() _processes = [ ] break return_stdout = '' return_stderr = '' error = False error_text = '' # Wait for all commands to complete # Switch how we monitor running processes / wait for them to complete # depending on whether or not the user has specified -info or -debug option try: if app.verbosity > 1: for process in _processes: stderrdata = b'' do_indent = True while True: # Have to read one character at a time: Waiting for a newline character using e.g. readline() will prevent MRtrix progressbars from appearing byte = process.stderr.read(1) stderrdata += byte char = byte.decode('cp1252', errors='ignore') if not char and process.poll() is not None: break if do_indent and char in string.printable and char != '\r' and char != '\n': sys.stderr.write(' ') do_indent = False elif char in [ '\r', '\n' ]: do_indent = True sys.stderr.write(char) sys.stderr.flush() stderrdata = stderrdata.decode('utf-8', errors='replace') return_stderr += stderrdata if process.returncode: error = True error_text += stderrdata else: for process in _processes: process.wait() except (KeyboardInterrupt, SystemExit): app.handler(signal.SIGINT, inspect.currentframe()) # Re-enable interrupt signal handler try: signal.signal(signal.SIGINT, app.handler) except: pass # For any command stdout / stderr data that wasn't either passed to another command or # printed to the terminal during execution, read it here. for index in range(len(cmdstack)): if tempfiles[index][0] is not None: tempfiles[index][0].flush() tempfiles[index][0].seek(0) stdout_text = tempfiles[index][0].read().decode('utf-8', errors='replace') return_stdout += stdout_text if _processes[index].returncode: error = True error_text += stdout_text if tempfiles[index][1] is not None: tempfiles[index][1].flush() tempfiles[index][1].seek(0) stderr_text = tempfiles[index][1].read().decode('utf-8', errors='replace') return_stderr += stderr_text if _processes[index].returncode: error = True error_text += stderr_text _processes = [ ] if error: if exitOnError: app.cleanup = False caller = inspect.getframeinfo(inspect.stack()[1][0]) script_name = os.path.basename(sys.argv[0]) app.console('') try: filename = caller.filename lineno = caller.lineno except AttributeError: filename = caller[1] lineno = caller[2] sys.stderr.write(script_name + ': ' + app.colourError + '[ERROR] Command failed: ' + cmd + app.colourClear + app.colourDebug + ' (' + os.path.basename(filename) + ':' + str(lineno) + ')' + app.colourClear + '\n') sys.stderr.write(script_name + ': ' + app.colourConsole + 'Output of failed command:' + app.colourClear + '\n') for line in error_text.splitlines(): sys.stderr.write(' ' * (len(script_name)+2) + line + '\n') app.console('') sys.stderr.flush() if app.tempDir: with open(os.path.join(app.tempDir, 'error.txt'), 'w') as outfile: outfile.write(cmd + '\n\n' + error_text + '\n') app.complete() sys.exit(1) else: app.warn('Command failed: ' + cmd) # Only now do we append to the script log, since the command has completed successfully # Note: Writing the command as it was formed as the input to run.command(): # other flags may potentially change if this file is eventually used to resume the script if app.tempDir: with open(os.path.join(app.tempDir, 'log.txt'), 'a') as outfile: outfile.write(cmd + '\n') return (return_stdout, return_stderr)
def execute(): #pylint: disable=unused-variable # Ideally want to use the oversampling-based regridding of the 5TT image from the SIFT model, not mrtransform # May need to commit 5ttregrid... # Verify input 5tt image verification_text = '' try: verification_text = run.command('5ttcheck 5tt.mif').stderr except run.MRtrixCmdError as except_5ttcheck: verification_text = except_5ttcheck.stderr if 'WARNING' in verification_text or 'ERROR' in verification_text: app.warn('Command 5ttcheck indicates problems with provided input 5TT image \'' + app.ARGS.in_5tt + '\':') for line in verification_text.splitlines(): app.warn(line) app.warn('These may or may not interfere with the dwi2response msmt_5tt script') # Get shell information shells = [ int(round(float(x))) for x in image.mrinfo('dwi.mif', 'shell_bvalues').split() ] if len(shells) < 3: app.warn('Less than three b-values; response functions will not be applicable in resolving three tissues using MSMT-CSD algorithm') # Get lmax information (if provided) wm_lmax = [ ] if app.ARGS.lmax: wm_lmax = [ int(x.strip()) for x in app.ARGS.lmax.split(',') ] if not len(wm_lmax) == len(shells): raise MRtrixError('Number of manually-defined lmax\'s (' + str(len(wm_lmax)) + ') does not match number of b-values (' + str(len(shells)) + ')') for shell_l in wm_lmax: if shell_l % 2: raise MRtrixError('Values for lmax must be even') if shell_l < 0: raise MRtrixError('Values for lmax must be non-negative') run.command('dwi2tensor dwi.mif - -mask mask.mif | tensor2metric - -fa fa.mif -vector vector.mif') if not os.path.exists('dirs.mif'): run.function(shutil.copy, 'vector.mif', 'dirs.mif') run.command('mrtransform 5tt.mif 5tt_regrid.mif -template fa.mif -interp linear') # Basic tissue masks run.command('mrconvert 5tt_regrid.mif - -coord 3 2 -axes 0,1,2 | mrcalc - ' + str(app.ARGS.pvf) + ' -gt mask.mif -mult wm_mask.mif') run.command('mrconvert 5tt_regrid.mif - -coord 3 0 -axes 0,1,2 | mrcalc - ' + str(app.ARGS.pvf) + ' -gt fa.mif ' + str(app.ARGS.fa) + ' -lt -mult mask.mif -mult gm_mask.mif') run.command('mrconvert 5tt_regrid.mif - -coord 3 3 -axes 0,1,2 | mrcalc - ' + str(app.ARGS.pvf) + ' -gt fa.mif ' + str(app.ARGS.fa) + ' -lt -mult mask.mif -mult csf_mask.mif') # Revise WM mask to only include single-fibre voxels recursive_cleanup_option='' if not app.DO_CLEANUP: recursive_cleanup_option = ' -nocleanup' if not app.ARGS.sfwm_fa_threshold: app.console('Selecting WM single-fibre voxels using \'' + app.ARGS.wm_algo + '\' algorithm') run.command('dwi2response ' + app.ARGS.wm_algo + ' dwi.mif wm_ss_response.txt -mask wm_mask.mif -voxels wm_sf_mask.mif -scratch ' + path.quote(app.SCRATCH_DIR) + recursive_cleanup_option) else: app.console('Selecting WM single-fibre voxels using \'fa\' algorithm with a hard FA threshold of ' + str(app.ARGS.sfwm_fa_threshold)) run.command('dwi2response fa dwi.mif wm_ss_response.txt -mask wm_mask.mif -threshold ' + str(app.ARGS.sfwm_fa_threshold) + ' -voxels wm_sf_mask.mif -scratch ' + path.quote(app.SCRATCH_DIR) + recursive_cleanup_option) # Check for empty masks wm_voxels = image.statistics('wm_sf_mask.mif', mask='wm_sf_mask.mif').count gm_voxels = image.statistics('gm_mask.mif', mask='gm_mask.mif').count csf_voxels = image.statistics('csf_mask.mif', mask='csf_mask.mif').count empty_masks = [ ] if not wm_voxels: empty_masks.append('WM') if not gm_voxels: empty_masks.append('GM') if not csf_voxels: empty_masks.append('CSF') if empty_masks: message = ','.join(empty_masks) message += ' tissue mask' if len(empty_masks) > 1: message += 's' message += ' empty; cannot estimate response function' if len(empty_masks) > 1: message += 's' raise MRtrixError(message) # For each of the three tissues, generate a multi-shell response bvalues_option = ' -shells ' + ','.join(map(str,shells)) sfwm_lmax_option = '' if wm_lmax: sfwm_lmax_option = ' -lmax ' + ','.join(map(str,wm_lmax)) run.command('amp2response dwi.mif wm_sf_mask.mif dirs.mif wm.txt' + bvalues_option + sfwm_lmax_option) run.command('amp2response dwi.mif gm_mask.mif dirs.mif gm.txt' + bvalues_option + ' -isotropic') run.command('amp2response dwi.mif csf_mask.mif dirs.mif csf.txt' + bvalues_option + ' -isotropic') run.function(shutil.copyfile, 'wm.txt', path.from_user(app.ARGS.out_wm, False)) run.function(shutil.copyfile, 'gm.txt', path.from_user(app.ARGS.out_gm, False)) run.function(shutil.copyfile, 'csf.txt', path.from_user(app.ARGS.out_csf, False)) # Generate output 4D binary image with voxel selections; RGB as in MSMT-CSD paper run.command('mrcat csf_mask.mif gm_mask.mif wm_sf_mask.mif voxels.mif -axis 3') if app.ARGS.voxels: run.command('mrconvert voxels.mif ' + path.from_user(app.ARGS.voxels), mrconvert_keyval=path.from_user(app.ARGS.input, False), force=app.FORCE_OVERWRITE)
def command(cmd, exitOnError=True): import inspect, itertools, os, shlex, subprocess, sys, tempfile from distutils.spawn import find_executable from mrtrix3 import app # This is the only global variable that is _modified_ within this function global _processes # Vectorise the command string, preserving anything encased within quotation marks cmdsplit = shlex.split(cmd) if app._lastFile: # Check to see if the last file produced in the previous script execution is # intended to be produced by this command; if it is, this will be the last # command that gets skipped by the -continue option # It's possible that the file might be defined in a '--option=XXX' style argument # It's also possible that the filename in the command string has the file extension omitted for entry in cmdsplit: if entry.startswith('--') and '=' in entry: cmdtotest = entry.split('=')[1] else: cmdtotest = entry filetotest = [ app._lastFile, os.path.splitext(app._lastFile)[0] ] if cmdtotest in filetotest: app.debug('Detected last file \'' + app._lastFile + '\' in command \'' + cmd + '\'; this is the last run.command() / run.function() call that will be skipped') app._lastFile = '' break if app._verbosity: sys.stderr.write(app.colourExec + 'Skipping command:' + app.colourClear + ' ' + cmd + '\n') sys.stderr.flush() return # This splits the command string based on the piping character '|', such that each # individual executable (along with its arguments) appears as its own list # Note that for Python2 support, it is necessary to convert groupby() output from # a generator to a list before it is passed to filter() cmdstack = [ list(g) for k, g in filter(lambda t : t[0], ((k, list(g)) for k, g in itertools.groupby(cmdsplit, lambda s : s is not '|') ) ) ] for line in cmdstack: is_mrtrix_exe = line[0] in _mrtrix_exe_list if is_mrtrix_exe: line[0] = versionMatch(line[0]) if app._nthreads is not None: line.extend( [ '-nthreads', str(app._nthreads) ] ) # Get MRtrix3 binaries to output additional INFO-level information if running in debug mode if app._verbosity == 3: line.append('-info') elif not app._verbosity: line.append('-quiet') else: line[0] = exeName(line[0]) shebang = _shebang(line[0]) if len(shebang): if not is_mrtrix_exe: # If a shebang is found, and this call is therefore invoking an # interpreter, can't rely on the interpreter finding the script # from PATH; need to find the full path ourselves. line[0] = find_executable(line[0]) for item in reversed(shebang): line.insert(0, item) if app._verbosity: sys.stderr.write(app.colourExec + 'Command:' + app.colourClear + ' ' + cmd + '\n') sys.stderr.flush() app.debug('To execute: ' + str(cmdstack)) # Construct temporary text files for holding stdout / stderr contents when appropriate # (One entry per process; each is a tuple containing two entries, each of which is either a # file-like object, or None) tempfiles = [ ] # Execute all processes _processes = [ ] for index, command in enumerate(cmdstack): file_out = None file_err = None # If there's at least one command prior to this, need to receive the stdout from the prior command # at the stdin of this command; otherwise, nothing to receive if index > 0: handle_in = _processes[index-1].stdout else: handle_in = None # If this is not the last command, then stdout needs to be piped to the next command; # otherwise, write stdout to a temporary file so that the contents can be read later if index < len(cmdstack)-1: handle_out = subprocess.PIPE else: file_out = tempfile.TemporaryFile() handle_out = file_out.fileno() # If we're in debug / info mode, the contents of stderr will be read and printed to the terminal # as the command progresses, hence this needs to go to a pipe; otherwise, write it to a temporary # file so that the contents can be read later if app._verbosity > 1: handle_err = subprocess.PIPE else: file_err = tempfile.TemporaryFile() handle_err = file_err.fileno() # Set off the processes try: process = subprocess.Popen (command, stdin=handle_in, stdout=handle_out, stderr=handle_err, env=_env) _processes.append(process) tempfiles.append( ( file_out, file_err ) ) # FileNotFoundError not defined in Python 2.7 except OSError as e: if exitOnError: app.error('\'' + command[0] + '\' not executed ("' + str(e) + '"); script cannot proceed') else: app.warn('\'' + command[0] + '\' not executed ("' + str(e) + '")') for p in _processes: p.terminate() _processes = [ ] break except (KeyboardInterrupt, SystemExit): import inspect, signal app._handler(signal.SIGINT, inspect.currentframe()) return_stdout = '' return_stderr = '' error = False error_text = '' # Wait for all commands to complete try: # Switch how we monitor running processes / wait for them to complete # depending on whether or not the user has specified -verbose or -debug option if app._verbosity > 1: for process in _processes: stderrdata = '' while True: # Have to read one character at a time: Waiting for a newline character using e.g. readline() will prevent MRtrix progressbars from appearing line = process.stderr.read(1).decode('utf-8') sys.stderr.write(line) sys.stderr.flush() stderrdata += line if not line and process.poll() is not None: break return_stderr += stderrdata if process.returncode: error = True error_text += stderrdata else: for process in _processes: process.wait() except (KeyboardInterrupt, SystemExit): import inspect, signal app._handler(signal.SIGINT, inspect.currentframe()) # For any command stdout / stderr data that wasn't either passed to another command or # printed to the terminal during execution, read it here. for index in range(len(cmdstack)): if tempfiles[index][0] is not None: tempfiles[index][0].flush() tempfiles[index][0].seek(0) stdout_text = tempfiles[index][0].read().decode('utf-8') return_stdout += stdout_text if _processes[index].returncode: error = True error_text += stdout_text if tempfiles[index][1] is not None: tempfiles[index][1].flush() tempfiles[index][1].seek(0) stderr_text = tempfiles[index][1].read().decode('utf-8') return_stderr += stderr_text if _processes[index].returncode: error = True error_text += stderr_text _processes = [ ] if (error): app._cleanup = False if exitOnError: caller = inspect.getframeinfo(inspect.stack()[1][0]) app.console('') sys.stderr.write(os.path.basename(sys.argv[0]) + ': ' + app.colourError + '[ERROR] Command failed: ' + cmd + app.colourClear + app.colourDebug + ' (' + os.path.basename(caller.filename) + ':' + str(caller.lineno) + ')' + app.colourClear + '\n') sys.stderr.write(os.path.basename(sys.argv[0]) + ': ' + app.colourConsole + 'Output of failed command:' + app.colourClear + '\n') sys.stderr.write(error_text) sys.stderr.flush() if app._tempDir: with open(os.path.join(app._tempDir, 'error.txt'), 'w') as outfile: outfile.write(cmd + '\n\n' + error_text + '\n') app.complete() sys.exit(1) else: app.warn('Command failed: ' + cmd) # Only now do we append to the script log, since the command has completed successfully # Note: Writing the command as it was formed as the input to run.command(): # other flags may potentially change if this file is eventually used to resume the script if app._tempDir: with open(os.path.join(app._tempDir, 'log.txt'), 'a') as outfile: outfile.write(cmd + '\n') return (return_stdout, return_stderr)
def execute(): import os from distutils.spawn import find_executable from mrtrix3 import app, file, fsl, image, path, run if app.isWindows(): app.error( '\'fsl\' algorithm of 5ttgen script cannot be run on Windows: FSL not available on Windows' ) fsl_path = os.environ.get('FSLDIR', '') if not fsl_path: app.error( 'Environment variable FSLDIR is not set; please run appropriate FSL configuration script' ) ssroi_cmd = 'standard_space_roi' if not find_executable(ssroi_cmd): ssroi_cmd = 'fsl5.0-standard_space_roi' if not find_executable(ssroi_cmd): app.error( 'Could not find FSL program standard_space_roi; please verify FSL install' ) bet_cmd = 'bet' if not find_executable(bet_cmd): bet_cmd = 'fsl5.0-bet' if not find_executable(bet_cmd): app.error( 'Could not find FSL program bet; please verify FSL install') fast_cmd = 'fast' if not find_executable(fast_cmd): fast_cmd = 'fsl5.0-fast' if not find_executable(fast_cmd): app.error( 'Could not find FSL program fast; please verify FSL install') first_cmd = 'run_first_all' if not find_executable(first_cmd): first_cmd = "fsl5.0-run_first_all" if not find_executable(first_cmd): app.error( 'Could not find FSL program run_first_all; please verify FSL install' ) first_atlas_path = os.path.join(fsl_path, 'data', 'first', 'models_336_bin') if not os.path.isdir(first_atlas_path): app.error( 'Atlases required for FSL\'s FIRST program not installed; please install fsl-first-data using your relevant package manager' ) fsl_suffix = fsl.suffix() sgm_structures = [ 'L_Accu', 'R_Accu', 'L_Caud', 'R_Caud', 'L_Pall', 'R_Pall', 'L_Puta', 'R_Puta', 'L_Thal', 'R_Thal' ] if app.args.sgm_amyg_hipp: sgm_structures.extend(['L_Amyg', 'R_Amyg', 'L_Hipp', 'R_Hipp']) run.command('mrconvert input.mif T1.nii -stride -1,+2,+3') fast_t1_input = 'T1.nii' fast_t2_input = '' # Decide whether or not we're going to do any brain masking if os.path.exists('mask.mif'): fast_t1_input = 'T1_masked' + fsl_suffix # Check to see if the mask matches the T1 image if image.match('T1.nii', 'mask.mif'): run.command('mrcalc T1.nii mask.mif -mult ' + fast_t1_input) mask_path = 'mask.mif' else: app.warn('Mask image does not match input image - re-gridding') run.command( 'mrtransform mask.mif mask_regrid.mif -template T1.nii') run.command('mrcalc T1.nii mask_regrid.mif ' + fast_t1_input) mask_path = 'mask_regrid.mif' if os.path.exists('T2.nii'): fast_t2_input = 'T2_masked' + fsl_suffix run.command('mrcalc T2.nii ' + mask_path + ' -mult ' + fast_t2_input) elif app.args.premasked: fast_t1_input = 'T1.nii' if os.path.exists('T2.nii'): fast_t2_input = 'T2.nii' else: # Use FSL command standard_space_roi to do an initial masking of the image before BET # Also reduce the FoV of the image # Using MNI 1mm dilated brain mask rather than the -b option in standard_space_roi (which uses the 2mm mask); the latter looks 'buggy' to me... Unfortunately even with the 1mm 'dilated' mask, it can still cut into some brain areas, hence the explicit dilation mni_mask_path = os.path.join(fsl_path, 'data', 'standard', 'MNI152_T1_1mm_brain_mask_dil.nii.gz') mni_mask_dilation = 0 if os.path.exists(mni_mask_path): mni_mask_dilation = 4 else: mni_mask_path = os.path.join( fsl_path, 'data', 'standard', 'MNI152_T1_2mm_brain_mask_dil.nii.gz') if os.path.exists(mni_mask_path): mni_mask_dilation = 2 if mni_mask_dilation: run.command('maskfilter ' + mni_mask_path + ' dilate mni_mask.nii -npass ' + str(mni_mask_dilation)) if app.args.nocrop: ssroi_roi_option = ' -roiNONE' else: ssroi_roi_option = ' -roiFOV' run.command( ssroi_cmd + ' T1.nii T1_preBET' + fsl_suffix + ' -maskMASK mni_mask.nii' + ssroi_roi_option, False) else: run.command(ssroi_cmd + ' T1.nii T1_preBET' + fsl_suffix + ' -b', False) pre_bet_image = fsl.findImage('T1_preBET') # BET run.command(bet_cmd + ' ' + pre_bet_image + ' T1_BET' + fsl_suffix + ' -f 0.15 -R') fast_t1_input = fsl.findImage('T1_BET' + fsl_suffix) if os.path.exists('T2.nii'): if app.args.nocrop: fast_t2_input = 'T2.nii' else: # Just a reduction of FoV, no sub-voxel interpolation going on run.command('mrtransform T2.nii T2_cropped.nii -template ' + fast_t1_input + ' -interp nearest') fast_t2_input = 'T2_cropped.nii' # Finish branching based on brain masking # FAST if fast_t2_input: run.command(fast_cmd + ' -S 2 ' + fast_t2_input + ' ' + fast_t1_input) else: run.command(fast_cmd + ' ' + fast_t1_input) # FIRST first_input_is_brain_extracted = '' if app.args.premasked: first_input_is_brain_extracted = ' -b' run.command(first_cmd + ' -m none -s ' + ','.join(sgm_structures) + ' -i T1.nii -o first' + first_input_is_brain_extracted) fsl.checkFirst('first', sgm_structures) # Convert FIRST meshes to partial volume images pve_image_list = [] for struct in sgm_structures: pve_image_path = 'mesh2pve_' + struct + '.mif' vtk_in_path = 'first-' + struct + '_first.vtk' vtk_temp_path = struct + '.vtk' run.command('meshconvert ' + vtk_in_path + ' ' + vtk_temp_path + ' -transform first2real T1.nii') run.command('mesh2pve ' + vtk_temp_path + ' ' + fast_t1_input + ' ' + pve_image_path) pve_image_list.append(pve_image_path) pve_cat = ' '.join(pve_image_list) run.command('mrmath ' + pve_cat + ' sum - | mrcalc - 1.0 -min all_sgms.mif') # Combine the tissue images into the 5TT format within the script itself fast_output_prefix = fast_t1_input.split('.')[0] fast_csf_output = fsl.findImage(fast_output_prefix + '_pve_0') fast_gm_output = fsl.findImage(fast_output_prefix + '_pve_1') fast_wm_output = fsl.findImage(fast_output_prefix + '_pve_2') # Step 1: Run LCC on the WM image run.command( 'mrthreshold ' + fast_wm_output + ' - -abs 0.001 | maskfilter - connect - -connectivity | mrcalc 1 - 1 -gt -sub remove_unconnected_wm_mask.mif -datatype bit' ) # Step 2: Generate the images in the same fashion as the old 5ttgen binary used to: # - Preserve CSF as-is # - Preserve SGM, unless it results in a sum of volume fractions greater than 1, in which case clamp # - Multiply the FAST volume fractions of GM and CSF, so that the sum of CSF, SGM, CGM and WM is 1.0 run.command('mrcalc ' + fast_csf_output + ' remove_unconnected_wm_mask.mif -mult csf.mif') run.command('mrcalc 1.0 csf.mif -sub all_sgms.mif -min sgm.mif') run.command('mrcalc 1.0 csf.mif sgm.mif -add -sub ' + fast_gm_output + ' ' + fast_wm_output + ' -add -div multiplier.mif') run.command( 'mrcalc multiplier.mif -finite multiplier.mif 0.0 -if multiplier_noNAN.mif' ) run.command( 'mrcalc ' + fast_gm_output + ' multiplier_noNAN.mif -mult remove_unconnected_wm_mask.mif -mult cgm.mif' ) run.command( 'mrcalc ' + fast_wm_output + ' multiplier_noNAN.mif -mult remove_unconnected_wm_mask.mif -mult wm.mif' ) run.command('mrcalc 0 wm.mif -min path.mif') run.command( 'mrcat cgm.mif sgm.mif wm.mif csf.mif path.mif - -axis 3 | mrconvert - combined_precrop.mif -stride +2,+3,+4,+1' ) # Use mrcrop to reduce file size (improves caching of image data during tracking) if app.args.nocrop: run.command('mrconvert combined_precrop.mif result.mif') else: run.command( 'mrmath combined_precrop.mif sum - -axis 3 | mrthreshold - - -abs 0.5 | mrcrop combined_precrop.mif result.mif -mask -' )
def execute(): #pylint: disable=unused-variable bzero_threshold = float( CONFIG['BZeroThreshold']) if 'BZeroThreshold' in CONFIG else 10.0 # CHECK INPUTS AND OPTIONS app.console('-------') # Get b-values and number of volumes per b-value. bvalues = [ int(round(float(x))) for x in image.mrinfo('dwi.mif', 'shell_bvalues').split() ] bvolumes = [int(x) for x in image.mrinfo('dwi.mif', 'shell_sizes').split()] app.console( str(len(bvalues)) + ' unique b-value(s) detected: ' + ','.join(map(str, bvalues)) + ' with ' + ','.join(map(str, bvolumes)) + ' volumes') if len(bvalues) < 2: raise MRtrixError('Need at least 2 unique b-values (including b=0).') bvalues_option = ' -shells ' + ','.join(map(str, bvalues)) # Get lmax information (if provided). sfwm_lmax = [] if app.ARGS.lmax: sfwm_lmax = [int(x.strip()) for x in app.ARGS.lmax.split(',')] if not len(sfwm_lmax) == len(bvalues): raise MRtrixError('Number of lmax\'s (' + str(len(sfwm_lmax)) + ', as supplied to the -lmax option: ' + ','.join(map(str, sfwm_lmax)) + ') does not match number of unique b-values.') for sfl in sfwm_lmax: if sfl % 2: raise MRtrixError( 'Values supplied to the -lmax option must be even.') if sfl < 0: raise MRtrixError( 'Values supplied to the -lmax option must be non-negative.' ) sfwm_lmax_option = '' if sfwm_lmax: sfwm_lmax_option = ' -lmax ' + ','.join(map(str, sfwm_lmax)) # PREPARATION app.console('-------') app.console('Preparation:') # Erode (brain) mask. if app.ARGS.erode > 0: app.console('* Eroding brain mask by ' + str(app.ARGS.erode) + ' pass(es)...') run.command('maskfilter mask.mif erode eroded_mask.mif -npass ' + str(app.ARGS.erode), show=False) else: app.console('Not eroding brain mask.') run.command('mrconvert mask.mif eroded_mask.mif -datatype bit', show=False) statmaskcount = image.statistics('mask.mif', mask='mask.mif').count statemaskcount = image.statistics('eroded_mask.mif', mask='eroded_mask.mif').count app.console(' [ mask: ' + str(statmaskcount) + ' -> ' + str(statemaskcount) + ' ]') # Get volumes, compute mean signal and SDM per b-value; compute overall SDM; get rid of erroneous values. app.console('* Computing signal decay metric (SDM):') totvolumes = 0 fullsdmcmd = 'mrcalc' errcmd = 'mrcalc' zeropath = 'mean_b' + str(bvalues[0]) + '.mif' for ibv, bval in enumerate(bvalues): app.console(' * b=' + str(bval) + '...') meanpath = 'mean_b' + str(bval) + '.mif' run.command('dwiextract dwi.mif -shells ' + str(bval) + ' - | mrcalc - 0 -max - | mrmath - mean ' + meanpath + ' -axis 3', show=False) errpath = 'err_b' + str(bval) + '.mif' run.command('mrcalc ' + meanpath + ' -finite ' + meanpath + ' 0 -if 0 -le ' + errpath + ' -datatype bit', show=False) errcmd += ' ' + errpath if ibv > 0: errcmd += ' -add' sdmpath = 'sdm_b' + str(bval) + '.mif' run.command('mrcalc ' + zeropath + ' ' + meanpath + ' -divide -log ' + sdmpath, show=False) totvolumes += bvolumes[ibv] fullsdmcmd += ' ' + sdmpath + ' ' + str(bvolumes[ibv]) + ' -mult' if ibv > 1: fullsdmcmd += ' -add' fullsdmcmd += ' ' + str(totvolumes) + ' -divide full_sdm.mif' run.command(fullsdmcmd, show=False) app.console('* Removing erroneous voxels from mask and correcting SDM...') run.command( 'mrcalc full_sdm.mif -finite full_sdm.mif 0 -if 0 -le err_sdm.mif -datatype bit', show=False) errcmd += ' err_sdm.mif -add 0 eroded_mask.mif -if safe_mask.mif -datatype bit' run.command(errcmd, show=False) run.command('mrcalc safe_mask.mif full_sdm.mif 0 -if 10 -min safe_sdm.mif', show=False) statsmaskcount = image.statistics('safe_mask.mif', mask='safe_mask.mif').count app.console(' [ mask: ' + str(statemaskcount) + ' -> ' + str(statsmaskcount) + ' ]') # CRUDE SEGMENTATION app.console('-------') app.console('Crude segmentation:') # Compute FA and principal eigenvectors; crude WM versus GM-CSF separation based on FA. app.console('* Crude WM versus GM-CSF separation (at FA=' + str(app.ARGS.fa) + ')...') run.command( 'dwi2tensor dwi.mif - -mask safe_mask.mif | tensor2metric - -fa safe_fa.mif -vector safe_vecs.mif -modulate none -mask safe_mask.mif', show=False) run.command('mrcalc safe_mask.mif safe_fa.mif 0 -if ' + str(app.ARGS.fa) + ' -gt crude_wm.mif -datatype bit', show=False) run.command( 'mrcalc crude_wm.mif 0 safe_mask.mif -if _crudenonwm.mif -datatype bit', show=False) statcrudewmcount = image.statistics('crude_wm.mif', mask='crude_wm.mif').count statcrudenonwmcount = image.statistics('_crudenonwm.mif', mask='_crudenonwm.mif').count app.console(' [ ' + str(statsmaskcount) + ' -> ' + str(statcrudewmcount) + ' (WM) & ' + str(statcrudenonwmcount) + ' (GM-CSF) ]') # Crude GM versus CSF separation based on SDM. app.console('* Crude GM versus CSF separation...') crudenonwmmedian = image.statistics('safe_sdm.mif', mask='_crudenonwm.mif').median run.command( 'mrcalc _crudenonwm.mif safe_sdm.mif ' + str(crudenonwmmedian) + ' -subtract 0 -if - | mrthreshold - - -mask _crudenonwm.mif | mrcalc _crudenonwm.mif - 0 -if crude_csf.mif -datatype bit', show=False) run.command( 'mrcalc crude_csf.mif 0 _crudenonwm.mif -if crude_gm.mif -datatype bit', show=False) statcrudegmcount = image.statistics('crude_gm.mif', mask='crude_gm.mif').count statcrudecsfcount = image.statistics('crude_csf.mif', mask='crude_csf.mif').count app.console(' [ ' + str(statcrudenonwmcount) + ' -> ' + str(statcrudegmcount) + ' (GM) & ' + str(statcrudecsfcount) + ' (CSF) ]') # REFINED SEGMENTATION app.console('-------') app.console('Refined segmentation:') # Refine WM: remove high SDM outliers. app.console('* Refining WM...') crudewmmedian = image.statistics('safe_sdm.mif', mask='crude_wm.mif').median run.command('mrcalc crude_wm.mif safe_sdm.mif ' + str(crudewmmedian) + ' -subtract -abs 0 -if _crudewm_sdmad.mif', show=False) crudewmmad = image.statistics('_crudewm_sdmad.mif', mask='crude_wm.mif').median crudewmoutlthresh = crudewmmedian + (1.4826 * crudewmmad * 2.0) run.command('mrcalc crude_wm.mif safe_sdm.mif 0 -if ' + str(crudewmoutlthresh) + ' -gt _crudewmoutliers.mif -datatype bit', show=False) run.command( 'mrcalc _crudewmoutliers.mif 0 crude_wm.mif -if refined_wm.mif -datatype bit', show=False) statrefwmcount = image.statistics('refined_wm.mif', mask='refined_wm.mif').count app.console(' [ WM: ' + str(statcrudewmcount) + ' -> ' + str(statrefwmcount) + ' ]') # Refine GM: separate safer GM from partial volumed voxels. app.console('* Refining GM...') crudegmmedian = image.statistics('safe_sdm.mif', mask='crude_gm.mif').median run.command('mrcalc crude_gm.mif safe_sdm.mif 0 -if ' + str(crudegmmedian) + ' -gt _crudegmhigh.mif -datatype bit', show=False) run.command( 'mrcalc _crudegmhigh.mif 0 crude_gm.mif -if _crudegmlow.mif -datatype bit', show=False) run.command( 'mrcalc _crudegmhigh.mif safe_sdm.mif ' + str(crudegmmedian) + ' -subtract 0 -if - | mrthreshold - - -mask _crudegmhigh.mif -invert | mrcalc _crudegmhigh.mif - 0 -if _crudegmhighselect.mif -datatype bit', show=False) run.command( 'mrcalc _crudegmlow.mif safe_sdm.mif ' + str(crudegmmedian) + ' -subtract -neg 0 -if - | mrthreshold - - -mask _crudegmlow.mif -invert | mrcalc _crudegmlow.mif - 0 -if _crudegmlowselect.mif -datatype bit', show=False) run.command( 'mrcalc _crudegmhighselect.mif 1 _crudegmlowselect.mif -if refined_gm.mif -datatype bit', show=False) statrefgmcount = image.statistics('refined_gm.mif', mask='refined_gm.mif').count app.console(' [ GM: ' + str(statcrudegmcount) + ' -> ' + str(statrefgmcount) + ' ]') # Refine CSF: recover lost CSF from crude WM SDM outliers, separate safer CSF from partial volumed voxels. app.console('* Refining CSF...') crudecsfmin = image.statistics('safe_sdm.mif', mask='crude_csf.mif').min run.command('mrcalc _crudewmoutliers.mif safe_sdm.mif 0 -if ' + str(crudecsfmin) + ' -gt 1 crude_csf.mif -if _crudecsfextra.mif -datatype bit', show=False) run.command( 'mrcalc _crudecsfextra.mif safe_sdm.mif ' + str(crudecsfmin) + ' -subtract 0 -if - | mrthreshold - - -mask _crudecsfextra.mif | mrcalc _crudecsfextra.mif - 0 -if refined_csf.mif -datatype bit', show=False) statrefcsfcount = image.statistics('refined_csf.mif', mask='refined_csf.mif').count app.console(' [ CSF: ' + str(statcrudecsfcount) + ' -> ' + str(statrefcsfcount) + ' ]') # FINAL VOXEL SELECTION AND RESPONSE FUNCTION ESTIMATION app.console('-------') app.console('Final voxel selection and response function estimation:') # Get final voxels for CSF response function estimation from refined CSF. app.console('* CSF:') app.console(' * Selecting final voxels (' + str(app.ARGS.csf) + '% of refined CSF)...') voxcsfcount = int(round(statrefcsfcount * app.ARGS.csf / 100.0)) run.command( 'mrcalc refined_csf.mif safe_sdm.mif 0 -if - | mrthreshold - - -top ' + str(voxcsfcount) + ' -ignorezero | mrcalc refined_csf.mif - 0 -if - -datatype bit | mrconvert - voxels_csf.mif -axes 0,1,2', show=False) statvoxcsfcount = image.statistics('voxels_csf.mif', mask='voxels_csf.mif').count app.console(' [ CSF: ' + str(statrefcsfcount) + ' -> ' + str(statvoxcsfcount) + ' ]') # Estimate CSF response function app.console(' * Estimating response function...') run.command( 'amp2response dwi.mif voxels_csf.mif safe_vecs.mif response_csf.txt' + bvalues_option + ' -isotropic', show=False) # Get final voxels for GM response function estimation from refined GM. app.console('* GM:') app.console(' * Selecting final voxels (' + str(app.ARGS.gm) + '% of refined GM)...') voxgmcount = int(round(statrefgmcount * app.ARGS.gm / 100.0)) refgmmedian = image.statistics('safe_sdm.mif', mask='refined_gm.mif').median run.command( 'mrcalc refined_gm.mif safe_sdm.mif ' + str(refgmmedian) + ' -subtract -abs 1 -add 0 -if - | mrthreshold - - -bottom ' + str(voxgmcount) + ' -ignorezero | mrcalc refined_gm.mif - 0 -if - -datatype bit | mrconvert - voxels_gm.mif -axes 0,1,2', show=False) statvoxgmcount = image.statistics('voxels_gm.mif', mask='voxels_gm.mif').count app.console(' [ GM: ' + str(statrefgmcount) + ' -> ' + str(statvoxgmcount) + ' ]') # Estimate GM response function app.console(' * Estimating response function...') run.command( 'amp2response dwi.mif voxels_gm.mif safe_vecs.mif response_gm.txt' + bvalues_option + ' -isotropic', show=False) # Get final voxels for single-fibre WM response function estimation from refined WM. app.console('* Single-fibre WM:') app.console(' * Selecting final voxels' + ('' if app.ARGS.wm_algo == 'tax' else (' (' + str(app.ARGS.sfwm) + '% of refined WM)')) + '...') voxsfwmcount = int(round(statrefwmcount * app.ARGS.sfwm / 100.0)) if app.ARGS.wm_algo: recursive_cleanup_option = '' if not app.DO_CLEANUP: recursive_cleanup_option = ' -nocleanup' app.console(' Selecting WM single-fibre voxels using \'' + app.ARGS.wm_algo + '\' algorithm') if app.ARGS.wm_algo == 'tax' and app.ARGS.sfwm != 0.5: app.warn( 'Single-fibre WM response function selection algorithm "tax" will not honour requested WM voxel percentage' ) run.command( 'dwi2response ' + app.ARGS.wm_algo + ' dwi.mif _respsfwmss.txt -mask refined_wm.mif -voxels voxels_sfwm.mif' + ('' if app.ARGS.wm_algo == 'tax' else (' -number ' + str(voxsfwmcount))) + ' -scratch ' + path.quote(app.SCRATCH_DIR) + recursive_cleanup_option, show=False) else: app.console( ' Selecting WM single-fibre voxels using built-in (Dhollander et al., 2019) algorithm' ) run.command('mrmath dwi.mif mean mean_sig.mif -axis 3', show=False) refwmcoef = image.statistics('mean_sig.mif', mask='refined_wm.mif').median * math.sqrt( 4.0 * math.pi) if sfwm_lmax: isiso = [lm == 0 for lm in sfwm_lmax] else: isiso = [bv < bzero_threshold for bv in bvalues] with open('ewmrf.txt', 'w') as ewr: for iis in isiso: if iis: ewr.write("%s 0 0 0\n" % refwmcoef) else: ewr.write("%s -%s %s -%s\n" % (refwmcoef, refwmcoef, refwmcoef, refwmcoef)) run.command( 'dwi2fod msmt_csd dwi.mif ewmrf.txt abs_ewm2.mif response_csf.txt abs_csf2.mif -mask refined_wm.mif -lmax 2,0' + bvalues_option, show=False) run.command( 'mrconvert abs_ewm2.mif - -coord 3 0 | mrcalc - abs_csf2.mif -add abs_sum2.mif', show=False) run.command( 'sh2peaks abs_ewm2.mif - -num 1 -mask refined_wm.mif | peaks2amp - - | mrcalc - abs_sum2.mif -divide - | mrconvert - metric_sfwm2.mif -coord 3 0 -axes 0,1,2', show=False) run.command( 'mrcalc refined_wm.mif metric_sfwm2.mif 0 -if - | mrthreshold - - -top ' + str(voxsfwmcount * 2) + ' -ignorezero | mrcalc refined_wm.mif - 0 -if - -datatype bit | mrconvert - refined_sfwm.mif -axes 0,1,2', show=False) run.command( 'dwi2fod msmt_csd dwi.mif ewmrf.txt abs_ewm6.mif response_csf.txt abs_csf6.mif -mask refined_sfwm.mif -lmax 6,0' + bvalues_option, show=False) run.command( 'mrconvert abs_ewm6.mif - -coord 3 0 | mrcalc - abs_csf6.mif -add abs_sum6.mif', show=False) run.command( 'sh2peaks abs_ewm6.mif - -num 1 -mask refined_sfwm.mif | peaks2amp - - | mrcalc - abs_sum6.mif -divide - | mrconvert - metric_sfwm6.mif -coord 3 0 -axes 0,1,2', show=False) run.command( 'mrcalc refined_sfwm.mif metric_sfwm6.mif 0 -if - | mrthreshold - - -top ' + str(voxsfwmcount) + ' -ignorezero | mrcalc refined_sfwm.mif - 0 -if - -datatype bit | mrconvert - voxels_sfwm.mif -axes 0,1,2', show=False) statvoxsfwmcount = image.statistics('voxels_sfwm.mif', mask='voxels_sfwm.mif').count app.console(' [ WM: ' + str(statrefwmcount) + ' -> ' + str(statvoxsfwmcount) + ' (single-fibre) ]') # Estimate SF WM response function app.console(' * Estimating response function...') run.command( 'amp2response dwi.mif voxels_sfwm.mif safe_vecs.mif response_sfwm.txt' + bvalues_option + sfwm_lmax_option, show=False) # OUTPUT AND SUMMARY app.console('-------') app.console('Generating outputs...') # Generate 4D binary images with voxel selections at major stages in algorithm (RGB: WM=blue, GM=green, CSF=red). run.command( 'mrcat crude_csf.mif crude_gm.mif crude_wm.mif check_crude.mif -axis 3', show=False) run.command( 'mrcat refined_csf.mif refined_gm.mif refined_wm.mif check_refined.mif -axis 3', show=False) run.command( 'mrcat voxels_csf.mif voxels_gm.mif voxels_sfwm.mif check_voxels.mif -axis 3', show=False) # Copy results to output files run.function(shutil.copyfile, 'response_sfwm.txt', path.from_user(app.ARGS.out_sfwm, False), show=False) run.function(shutil.copyfile, 'response_gm.txt', path.from_user(app.ARGS.out_gm, False), show=False) run.function(shutil.copyfile, 'response_csf.txt', path.from_user(app.ARGS.out_csf, False), show=False) if app.ARGS.voxels: run.command('mrconvert check_voxels.mif ' + path.from_user(app.ARGS.voxels), mrconvert_keyval=path.from_user(app.ARGS.input, False), force=app.FORCE_OVERWRITE, show=False) app.console('-------')
def execute(): #pylint: disable=unused-variable import math, os from distutils.spawn import find_executable from mrtrix3 import app, fsl, image, MRtrixError, path, run, utils if utils.is_windows(): raise MRtrixError( '\'fsl\' algorithm of 5ttgen script cannot be run on Windows: FSL not available on Windows' ) fsl_path = os.environ.get('FSLDIR', '') if not fsl_path: raise MRtrixError( 'Environment variable FSLDIR is not set; please run appropriate FSL configuration script' ) bet_cmd = fsl.exe_name('bet') fast_cmd = fsl.exe_name('fast') first_cmd = fsl.exe_name('run_first_all') ssroi_cmd = fsl.exe_name('standard_space_roi') first_atlas_path = os.path.join(fsl_path, 'data', 'first', 'models_336_bin') if not os.path.isdir(first_atlas_path): raise MRtrixError( 'Atlases required for FSL\'s FIRST program not installed; please install fsl-first-data using your relevant package manager' ) fsl_suffix = fsl.suffix() sgm_structures = [ 'L_Accu', 'R_Accu', 'L_Caud', 'R_Caud', 'L_Pall', 'R_Pall', 'L_Puta', 'R_Puta', 'L_Thal', 'R_Thal' ] if app.ARGS.sgm_amyg_hipp: sgm_structures.extend(['L_Amyg', 'R_Amyg', 'L_Hipp', 'R_Hipp']) t1_spacing = image.Header('input.mif').spacing() upsample_for_first = False # If voxel size is 1.25mm or larger, make a guess that the user has erroneously re-gridded their data if math.pow(t1_spacing[0] * t1_spacing[1] * t1_spacing[2], 1.0 / 3.0) > 1.225: app.warn( 'Voxel size larger than expected for T1-weighted images (' + str(t1_spacing) + '); ' 'note that ACT does not require re-gridding of T1 image to DWI space, and indeed ' 'retaining the original higher resolution of the T1 image is preferable' ) upsample_for_first = True run.command('mrconvert input.mif T1.nii -strides -1,+2,+3') fast_t1_input = 'T1.nii' fast_t2_input = '' # Decide whether or not we're going to do any brain masking if os.path.exists('mask.mif'): fast_t1_input = 'T1_masked' + fsl_suffix # Check to see if the mask matches the T1 image if image.match('T1.nii', 'mask.mif'): run.command('mrcalc T1.nii mask.mif -mult ' + fast_t1_input) mask_path = 'mask.mif' else: app.warn('Mask image does not match input image - re-gridding') run.command( 'mrtransform mask.mif mask_regrid.mif -template T1.nii -datatype bit' ) run.command('mrcalc T1.nii mask_regrid.mif -mult ' + fast_t1_input) mask_path = 'mask_regrid.mif' if os.path.exists('T2.nii'): fast_t2_input = 'T2_masked' + fsl_suffix run.command('mrcalc T2.nii ' + mask_path + ' -mult ' + fast_t2_input) elif app.ARGS.premasked: fast_t1_input = 'T1.nii' if os.path.exists('T2.nii'): fast_t2_input = 'T2.nii' else: # Use FSL command standard_space_roi to do an initial masking of the image before BET # Also reduce the FoV of the image # Using MNI 1mm dilated brain mask rather than the -b option in standard_space_roi (which uses the 2mm mask); the latter looks 'buggy' to me... Unfortunately even with the 1mm 'dilated' mask, it can still cut into some brain areas, hence the explicit dilation mni_mask_path = os.path.join(fsl_path, 'data', 'standard', 'MNI152_T1_1mm_brain_mask_dil.nii.gz') mni_mask_dilation = 0 if os.path.exists(mni_mask_path): mni_mask_dilation = 4 else: mni_mask_path = os.path.join( fsl_path, 'data', 'standard', 'MNI152_T1_2mm_brain_mask_dil.nii.gz') if os.path.exists(mni_mask_path): mni_mask_dilation = 2 try: if mni_mask_dilation: run.command('maskfilter ' + mni_mask_path + ' dilate mni_mask.nii -npass ' + str(mni_mask_dilation)) if app.ARGS.nocrop: ssroi_roi_option = ' -roiNONE' else: ssroi_roi_option = ' -roiFOV' run.command(ssroi_cmd + ' T1.nii T1_preBET' + fsl_suffix + ' -maskMASK mni_mask.nii' + ssroi_roi_option) else: run.command(ssroi_cmd + ' T1.nii T1_preBET' + fsl_suffix + ' -b') except run.MRtrixCmdError: pass try: pre_bet_image = fsl.find_image('T1_preBET') except MRtrixError: app.warn('FSL script \'standard_space_roi\' did not complete successfully' + \ ('' if find_executable('dc') else ' (possibly due to program \'dc\' not being installed') + '; ' + \ 'attempting to continue by providing un-cropped image to BET') pre_bet_image = 'T1.nii' # BET run.command(bet_cmd + ' ' + pre_bet_image + ' T1_BET' + fsl_suffix + ' -f 0.15 -R') fast_t1_input = fsl.find_image('T1_BET' + fsl_suffix) if os.path.exists('T2.nii'): if app.ARGS.nocrop: fast_t2_input = 'T2.nii' else: # Just a reduction of FoV, no sub-voxel interpolation going on run.command('mrtransform T2.nii T2_cropped.nii -template ' + fast_t1_input + ' -interp nearest') fast_t2_input = 'T2_cropped.nii' # Finish branching based on brain masking # FAST if fast_t2_input: run.command(fast_cmd + ' -S 2 ' + fast_t2_input + ' ' + fast_t1_input) else: run.command(fast_cmd + ' ' + fast_t1_input) # FIRST first_input = 'T1.nii' if upsample_for_first: app.warn( 'Generating 1mm isotropic T1 image for FIRST in hope of preventing failure, since input image is of lower resolution' ) run.command('mrgrid T1.nii regrid T1_1mm.nii -voxel 1.0 -interp sinc') first_input = 'T1_1mm.nii' first_brain_extracted_option = '' if app.ARGS.premasked: first_brain_extracted_option = ' -b' first_debug_option = '' if not app.DO_CLEANUP: first_debug_option = ' -d' first_verbosity_option = '' if app.VERBOSITY == 3: first_verbosity_option = ' -v' run.command(first_cmd + ' -m none -s ' + ','.join(sgm_structures) + ' -i ' + first_input + ' -o first' + first_brain_extracted_option + first_debug_option + first_verbosity_option) fsl.check_first('first', sgm_structures) # Convert FIRST meshes to partial volume images pve_image_list = [] progress = app.ProgressBar( 'Generating partial volume images for SGM structures', len(sgm_structures)) for struct in sgm_structures: pve_image_path = 'mesh2voxel_' + struct + '.mif' vtk_in_path = 'first-' + struct + '_first.vtk' vtk_temp_path = struct + '.vtk' run.command('meshconvert ' + vtk_in_path + ' ' + vtk_temp_path + ' -transform first2real ' + first_input) run.command('mesh2voxel ' + vtk_temp_path + ' ' + fast_t1_input + ' ' + pve_image_path) pve_image_list.append(pve_image_path) progress.increment() progress.done() run.command(['mrmath', pve_image_list, 'sum', '-', '|', \ 'mrcalc', '-', '1.0', '-min', 'all_sgms.mif']) # Combine the tissue images into the 5TT format within the script itself fast_output_prefix = fast_t1_input.split('.')[0] fast_csf_output = fsl.find_image(fast_output_prefix + '_pve_0') fast_gm_output = fsl.find_image(fast_output_prefix + '_pve_1') fast_wm_output = fsl.find_image(fast_output_prefix + '_pve_2') # Step 1: Run LCC on the WM image run.command( 'mrthreshold ' + fast_wm_output + ' - -abs 0.001 | maskfilter - connect - -connectivity | mrcalc 1 - 1 -gt -sub remove_unconnected_wm_mask.mif -datatype bit' ) # Step 2: Generate the images in the same fashion as the old 5ttgen binary used to: # - Preserve CSF as-is # - Preserve SGM, unless it results in a sum of volume fractions greater than 1, in which case clamp # - Multiply the FAST volume fractions of GM and CSF, so that the sum of CSF, SGM, CGM and WM is 1.0 run.command('mrcalc ' + fast_csf_output + ' remove_unconnected_wm_mask.mif -mult csf.mif') run.command('mrcalc 1.0 csf.mif -sub all_sgms.mif -min sgm.mif') run.command('mrcalc 1.0 csf.mif sgm.mif -add -sub ' + fast_gm_output + ' ' + fast_wm_output + ' -add -div multiplier.mif') run.command( 'mrcalc multiplier.mif -finite multiplier.mif 0.0 -if multiplier_noNAN.mif' ) run.command( 'mrcalc ' + fast_gm_output + ' multiplier_noNAN.mif -mult remove_unconnected_wm_mask.mif -mult cgm.mif' ) run.command( 'mrcalc ' + fast_wm_output + ' multiplier_noNAN.mif -mult remove_unconnected_wm_mask.mif -mult wm.mif' ) run.command('mrcalc 0 wm.mif -min path.mif') run.command( 'mrcat cgm.mif sgm.mif wm.mif csf.mif path.mif - -axis 3 | mrconvert - combined_precrop.mif -strides +2,+3,+4,+1' ) # Crop to reduce file size (improves caching of image data during tracking) if app.ARGS.nocrop: run.function(os.rename, 'combined_precrop.mif', 'result.mif') else: run.command( 'mrmath combined_precrop.mif sum - -axis 3 | mrthreshold - - -abs 0.5 | mrgrid combined_precrop.mif crop result.mif -mask -' ) run.command('mrconvert result.mif ' + path.from_user(app.ARGS.output), mrconvert_keyval=path.from_user(app.ARGS.input), force=app.FORCE_OVERWRITE)
def execute(): import os from distutils.spawn import find_executable from mrtrix3 import app, file, fsl, image, run if app.isWindows(): app.error( '\'fsl\' algorithm of 5ttgen script cannot be run on Windows: FSL not available on Windows' ) fsl_path = os.environ.get('FSLDIR', '') if not fsl_path: app.error( 'Environment variable FSLDIR is not set; please run appropriate FSL configuration script' ) ssroi_cmd = 'standard_space_roi' if not find_executable(ssroi_cmd): ssroi_cmd = 'fsl5.0-standard_space_roi' if not find_executable(ssroi_cmd): app.error( 'Could not find FSL program standard_space_roi; please verify FSL install' ) bet_cmd = 'bet' if not find_executable(bet_cmd): bet_cmd = 'fsl5.0-bet' if not find_executable(bet_cmd): app.error( 'Could not find FSL program bet; please verify FSL install') fast_cmd = 'fast' if not find_executable(fast_cmd): fast_cmd = 'fsl5.0-fast' if not find_executable(fast_cmd): app.error( 'Could not find FSL program fast; please verify FSL install') first_cmd = 'run_first_all' if not find_executable(first_cmd): first_cmd = "fsl5.0-run_first_all" if not find_executable(first_cmd): app.error( 'Could not find FSL program run_first_all; please verify FSL install' ) first_atlas_path = os.path.join(fsl_path, 'data', 'first', 'models_336_bin') if not os.path.isdir(first_atlas_path): app.error( 'Atlases required for FSL\'s FIRST program not installed; please install fsl-first-data using your relevant package manager' ) fsl_suffix = fsl.suffix() sgm_structures = [ 'L_Accu', 'R_Accu', 'L_Caud', 'R_Caud', 'L_Pall', 'R_Pall', 'L_Puta', 'R_Puta', 'L_Thal', 'R_Thal' ] if app.args.sgm_amyg_hipp: sgm_structures.extend(['L_Amyg', 'R_Amyg', 'L_Hipp', 'R_Hipp']) run.command('mrconvert input.mif T1.nii -stride -1,+2,+3') fast_t1_input = 'T1.nii' fast_t2_input = '' # Decide whether or not we're going to do any brain masking if os.path.exists('mask.mif'): fast_t1_input = 'T1_masked' + fsl_suffix # Check to see if the mask matches the T1 image if image.match('T1.nii', 'mask.mif'): run.command('mrcalc T1.nii mask.mif -mult ' + fast_t1_input) mask_path = 'mask.mif' else: app.warn('Mask image does not match input image - re-gridding') run.command( 'mrtransform mask.mif mask_regrid.mif -template T1.nii') run.command('mrcalc T1.nii mask_regrid.mif ' + fast_t1_input) mask_path = 'mask_regrid.mif' if os.path.exists('T2.nii'): fast_t2_input = 'T2_masked' + fsl_suffix run.command('mrcalc T2.nii ' + mask_path + ' -mult ' + fast_t2_input) elif app.args.premasked: fast_t1_input = 'T1.nii' if os.path.exists('T2.nii'): fast_t2_input = 'T2.nii' else: # Use FSL command standard_space_roi to do an initial masking of the image before BET # Also reduce the FoV of the image # Using MNI 1mm dilated brain mask rather than the -b option in standard_space_roi (which uses the 2mm mask); the latter looks 'buggy' to me... Unfortunately even with the 1mm 'dilated' mask, it can still cut into some brain areas, hence the explicit dilation mni_mask_path = os.path.join(fsl_path, 'data', 'standard', 'MNI152_T1_1mm_brain_mask_dil.nii.gz') mni_mask_dilation = 0 if os.path.exists(mni_mask_path): mni_mask_dilation = 4 else: mni_mask_path = os.path.join( fsl_path, 'data', 'standard', 'MNI152_T1_2mm_brain_mask_dil.nii.gz') if os.path.exists(mni_mask_path): mni_mask_dilation = 2 if mni_mask_dilation: run.command('maskfilter ' + mni_mask_path + ' dilate mni_mask.nii -npass ' + str(mni_mask_dilation)) if app.args.nocrop: ssroi_roi_option = ' -roiNONE' else: ssroi_roi_option = ' -roiFOV' run.command( ssroi_cmd + ' T1.nii T1_preBET' + fsl_suffix + ' -maskMASK mni_mask.nii' + ssroi_roi_option, False) else: run.command(ssroi_cmd + ' T1.nii T1_preBET' + fsl_suffix + ' -b', False) # For whatever reason, the output file from standard_space_roi may not be # completed before BET is run file.waitFor('T1_preBET' + fsl_suffix) # BET fast_t1_input = 'T1_BET' + fsl_suffix run.command(bet_cmd + ' T1_preBET' + fsl_suffix + ' ' + fast_t1_input + ' -f 0.15 -R') if os.path.exists('T2.nii'): if app.args.nocrop: fast_t2_input = 'T2.nii' else: # Just a reduction of FoV, no sub-voxel interpolation going on run.command('mrtransform T2.nii T2_cropped.nii -template ' + fast_t1_input + ' -interp nearest') fast_t2_input = 'T2_cropped.nii' # Finish branching based on brain masking # FAST if fast_t2_input: run.command(fast_cmd + ' -S 2 ' + fast_t2_input + ' ' + fast_t1_input) else: run.command(fast_cmd + ' ' + fast_t1_input) fast_output_prefix = fast_t1_input.split('.')[0] # FIRST first_input_is_brain_extracted = '' if app.args.premasked: first_input_is_brain_extracted = ' -b' run.command(first_cmd + ' -s ' + ','.join(sgm_structures) + ' -i T1.nii -o first' + first_input_is_brain_extracted) # Test to see whether or not FIRST has succeeded # However if the expected image is absent, it may be due to FIRST being run # on SGE; in this case it is necessary to wait and see if the file appears. # But even in this case, FIRST may still fail, and the file will never appear... combined_image_path = 'first_all_none_firstseg' + fsl_suffix if not os.path.isfile(combined_image_path): if 'SGE_ROOT' in os.environ: app.console( 'FSL FIRST job has been submitted to SGE; awaiting completion') app.console( '(note however that FIRST may fail, and hence this script may hang indefinitely)' ) file.waitFor(combined_image_path) else: app.error( 'FSL FIRST has failed; not all structures were segmented successfully (check ' + path.toTemp('first.logs', False) + ')') # Convert FIRST meshes to partial volume images pve_image_list = [] for struct in sgm_structures: pve_image_path = 'mesh2pve_' + struct + '.mif' vtk_in_path = 'first-' + struct + '_first.vtk' vtk_temp_path = struct + '.vtk' run.command('meshconvert ' + vtk_in_path + ' ' + vtk_temp_path + ' -transform first2real T1.nii') run.command('mesh2pve ' + vtk_temp_path + ' ' + fast_t1_input + ' ' + pve_image_path) pve_image_list.append(pve_image_path) pve_cat = ' '.join(pve_image_list) run.command('mrmath ' + pve_cat + ' sum - | mrcalc - 1.0 -min all_sgms.mif') # Looks like FAST in 5.0 ignores FSLOUTPUTTYPE when writing the PVE images # Will have to wait and see whether this changes, and update the script accordingly if fast_cmd == 'fast': fast_suffix = fsl_suffix else: fast_suffix = '.nii.gz' # Combine the tissue images into the 5TT format within the script itself # Step 1: Run LCC on the WM image run.command( 'mrthreshold ' + fast_output_prefix + '_pve_2' + fast_suffix + ' - -abs 0.001 | maskfilter - connect - -connectivity | mrcalc 1 - 1 -gt -sub remove_unconnected_wm_mask.mif -datatype bit' ) # Step 2: Generate the images in the same fashion as the 5ttgen command run.command('mrcalc ' + fast_output_prefix + '_pve_0' + fast_suffix + ' remove_unconnected_wm_mask.mif -mult csf.mif') run.command('mrcalc 1.0 csf.mif -sub all_sgms.mif -min sgm.mif') run.command('mrcalc 1.0 csf.mif sgm.mif -add -sub ' + fast_output_prefix + '_pve_1' + fast_suffix + ' ' + fast_output_prefix + '_pve_2' + fast_suffix + ' -add -div multiplier.mif') run.command( 'mrcalc multiplier.mif -finite multiplier.mif 0.0 -if multiplier_noNAN.mif' ) run.command( 'mrcalc ' + fast_output_prefix + '_pve_1' + fast_suffix + ' multiplier_noNAN.mif -mult remove_unconnected_wm_mask.mif -mult cgm.mif' ) run.command( 'mrcalc ' + fast_output_prefix + '_pve_2' + fast_suffix + ' multiplier_noNAN.mif -mult remove_unconnected_wm_mask.mif -mult wm.mif' ) run.command('mrcalc 0 wm.mif -min path.mif') run.command( 'mrcat cgm.mif sgm.mif wm.mif csf.mif path.mif - -axis 3 | mrconvert - combined_precrop.mif -stride +2,+3,+4,+1' ) # Use mrcrop to reduce file size (improves caching of image data during tracking) if app.args.nocrop: run.command('mrconvert combined_precrop.mif result.mif') else: run.command( 'mrmath combined_precrop.mif sum - -axis 3 | mrthreshold - - -abs 0.5 | mrcrop combined_precrop.mif result.mif -mask -' )
def execute(): import math, os, shutil from mrtrix3 import app, image, path, run # Ideally want to use the oversampling-based regridding of the 5TT image from the SIFT model, not mrtransform # May need to commit 5ttregrid... # Verify input 5tt image run.command('5ttcheck 5tt.mif', False) # Get shell information shells = [ int(round(float(x))) for x in image.headerField('dwi.mif', 'shells').split() ] if len(shells) < 3: app.warn('Less than three b-value shells; response functions will not be applicable in resolving three tissues using MSMT-CSD algorithm') # Get lmax information (if provided) wm_lmax = [ ] if app.args.lmax: wm_lmax = [ int(x.strip()) for x in app.args.lmax.split(',') ] if not len(wm_lmax) == len(shells): app.error('Number of manually-defined lmax\'s (' + str(len(wm_lmax)) + ') does not match number of b-value shells (' + str(len(shells)) + ')') for l in wm_lmax: if l%2: app.error('Values for lmax must be even') if l<0: app.error('Values for lmax must be non-negative') run.command('dwi2tensor dwi.mif - -mask mask.mif | tensor2metric - -fa fa.mif -vector vector.mif') if not os.path.exists('dirs.mif'): run.function(shutil.copy, 'vector.mif', 'dirs.mif') run.command('mrtransform 5tt.mif 5tt_regrid.mif -template fa.mif -interp linear') # Basic tissue masks run.command('mrconvert 5tt_regrid.mif - -coord 3 2 -axes 0,1,2 | mrcalc - ' + str(app.args.pvf) + ' -gt mask.mif -mult wm_mask.mif') run.command('mrconvert 5tt_regrid.mif - -coord 3 0 -axes 0,1,2 | mrcalc - ' + str(app.args.pvf) + ' -gt fa.mif ' + str(app.args.fa) + ' -lt -mult mask.mif -mult gm_mask.mif') run.command('mrconvert 5tt_regrid.mif - -coord 3 3 -axes 0,1,2 | mrcalc - ' + str(app.args.pvf) + ' -gt fa.mif ' + str(app.args.fa) + ' -lt -mult mask.mif -mult csf_mask.mif') # Revise WM mask to only include single-fibre voxels app.console('Calling dwi2response recursively to select WM single-fibre voxels using \'' + app.args.wm_algo + '\' algorithm') recursive_cleanup_option='' if not app._cleanup: recursive_cleanup_option = ' -nocleanup' run.command('dwi2response ' + app.args.wm_algo + ' dwi.mif wm_ss_response.txt -mask wm_mask.mif -voxels wm_sf_mask.mif -tempdir ' + app._tempDir + recursive_cleanup_option) # Check for empty masks wm_voxels = int(image.statistic('wm_sf_mask.mif', 'count', 'wm_sf_mask.mif')) gm_voxels = int(image.statistic('gm_mask.mif', 'count', 'gm_mask.mif')) csf_voxels = int(image.statistic('csf_mask.mif', 'count', 'csf_mask.mif')) empty_masks = [ ] if not wm_voxels: empty_masks.append('WM') if not gm_voxels: empty_masks.append('GM') if not csf_voxels: empty_masks.append('CSF') if empty_masks: message = ','.join(empty_masks) message += ' tissue mask' if len(empty_masks) > 1: message += 's' message += ' empty; cannot estimate response function' if len(empty_masks) > 1: message += 's' app.error(message) # For each of the three tissues, generate a multi-shell response bvalues_option = ' -shell ' + ','.join(map(str,shells)) sfwm_lmax_option = '' if wm_lmax: sfwm_lmax_option = ' -lmax ' + ','.join(map(str,wm_lmax)) run.command('amp2response dwi.mif wm_sf_mask.mif dirs.mif wm.txt' + bvalues_option + sfwm_lmax_option) run.command('amp2response dwi.mif gm_mask.mif dirs.mif gm.txt' + bvalues_option + ' -isotropic') run.command('amp2response dwi.mif csf_mask.mif dirs.mif csf.txt' + bvalues_option + ' -isotropic') run.function(shutil.copyfile, 'wm.txt', path.fromUser(app.args.out_wm, False)) run.function(shutil.copyfile, 'gm.txt', path.fromUser(app.args.out_gm, False)) run.function(shutil.copyfile, 'csf.txt', path.fromUser(app.args.out_csf, False)) # Generate output 4D binary image with voxel selections; RGB as in MSMT-CSD paper run.command('mrcat csf_mask.mif gm_mask.mif wm_sf_mask.mif voxels.mif -axis 3')