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 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 is_hidden(directory, filename):
if utils.is_windows():
try:
attrs = ctypes.windll.kernel32.GetFileAttributesW(u"%s" % str(os.path.join(directory, filename)))
assert attrs != -1
return bool(attrs & 2)
except (AttributeError, AssertionError):
return filename.startswith('.')
return filename.startswith('.')
def _shebang(item):
import os
from distutils.spawn import find_executable
from mrtrix3 import app, MRtrixError, utils
# 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(' ')
if utils.is_windows():
# 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
if os.path.basename(shebang[0]) == 'env':
new_shebang = [
os.path.abspath(find_executable(exe_name(shebang[1])))
]
new_shebang.extend(shebang[2:])
shebang = new_shebang
else:
new_shebang = [
os.path.abspath(
find_executable(
exe_name(os.path.basename(shebang[0]))))
]
new_shebang.extend(shebang[1:])
shebang = new_shebang
if not shebang or not shebang[0]:
raise MRtrixError('malformed shebang in file \"' + item +
'\": \"' + line + '\"')
app.debug('File \"' + item + '\": string \"' + line + '\": ' +
str(shebang))
return shebang
app.debug('File \"' + item + '\": No shebang found')
return []
def in_use(path):
if not os.path.isfile(path):
return None
if utils.is_windows():
if not os.access(path, os.W_OK):
return None
try:
with open(path, 'rb+') as dummy_f:
pass
return False
except:
return True
if not find_executable('fuser'):
return None
# fuser returns zero if there IS at least one process accessing the file
# A fatal error will result in a non-zero code -> in_use() = False, so wait_for() can return
return not subprocess.call(['fuser', '-s', path], shell=False, stdin=None, stdout=None, stderr=None)
def exe_name(item):
from mrtrix3 import app, utils #pylint: disable=import-outside-toplevel
if not utils.is_windows():
path = item
elif item.endswith('.exe'):
path = item
elif os.path.isfile(os.path.join(BIN_PATH, item)):
path = item
elif os.path.isfile(os.path.join(BIN_PATH, item + '.exe')):
path = item + '.exe'
elif find_executable(item) is not None:
path = item
elif find_executable(item + '.exe') is not None:
path = item + '.exe'
# If it can't be found, return the item as-is; find_executable() fails to identify Python scripts
else:
path = item
app.debug(item + ' -> ' + path)
return path
'SIGBUS' : 'Bus error: Accessing invalid address (out of storage space?)',
'SIGFPE' : 'Floating-point arithmetic exception',
'SIGHUP' : 'Disconnection of terminal',
'SIGILL' : 'Illegal instruction (corrupt binary command file?)',
'SIGINT' : 'Program manually interrupted by terminal',
'SIGPIPE': 'Nothing on receiving end of pipe',
'SIGPWR' : 'Power failure restart',
'SIGQUIT': 'Received terminal quit signal',
'SIGSEGV': 'Segmentation fault: Invalid memory reference',
'SIGSYS' : 'Bad system call',
'SIGXCPU': 'CPU time limit exceeded',
'SIGXFSZ': 'File size limit exceeded' }
# Can't be handled; see https://bugs.python.org/issue9524
# 'CTRL_C_EVENT': 'Terminated by user Ctrl-C input',
# 'CTRL_BREAK_EVENT': 'Terminated by user Ctrl-Break input'
if utils.is_windows():
_SIGNALS['SIGBREAK'] = 'Received Windows \'break\' signal'
else:
_SIGNALS['SIGTERM'] = 'Received termination signal'
# Generally preferable to use:
# "import mrtrix3"
# "mrtrix3.execute()"
# , rather than executing this function directly
def _execute(module): #pylint: disable=unused-variable
from mrtrix3 import run #pylint: disable=import-outside-toplevel
global ARGS, CMDLINE, CONTINUE_OPTION, DO_CLEANUP, EXEC_NAME, FORCE_OVERWRITE, NUM_THREADS, SCRATCH_DIR, VERBOSITY, WORKING_DIR
# Set up signal handlers
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)
