def complete():
import os, shutil, sys
from lib.printMessage import printMessage
global tempDir, workingDir
printMessage('Changing back to original directory (' + workingDir + ')')
os.chdir(workingDir)
if cleanup and tempDir:
printMessage('Deleting temporary directory ' + tempDir)
shutil.rmtree(tempDir)
elif tempDir:
# This needs to be printed even if the -quiet option is used
if os.path.isfile(os.path.join(tempDir, 'error.txt')):
with open(os.path.join(tempDir, 'error.txt'), 'rb') as errortext:
sys.stdout.write(
os.path.basename(sys.argv[0]) + ': ' + colourWarn +
'Script failed while executing the command: ' +
errortext.readline().rstrip() + colourClear + '\n')
sys.stdout.write(
os.path.basename(sys.argv[0]) + ': ' + colourWarn +
'For debugging, inspect contents of temporary directory: ' +
tempDir + colourClear + '\n')
else:
sys.stdout.write(
os.path.basename(sys.argv[0]) + ': ' + colourPrint +
'Contents of temporary directory kept, location: ' + tempDir +
colourClear + '\n')
sys.stdout.flush()
def delFile(path):
import lib.app, os
from lib.printMessage import printMessage
if not lib.app.cleanup:
return
printMessage('Deleting file: ' + path)
os.remove(path)
def makeTempDir():
import os, random, string, sys
from lib.errorMessage import errorMessage
from lib.printMessage import printMessage
from lib.readMRtrixConfSetting import readMRtrixConfSetting
global args, tempDir
if args.cont:
printMessage('Skipping temporary directory creation due to use of -continue option')
return
if tempDir:
errorMessage('Script error: Cannot use multiple temporary directories')
if args.tempdir:
dir_path = os.path.abspath(args.tempdir)
else:
dir_path = readMRtrixConfSetting('TmpFileDir')
if not dir_path:
if os.name == 'posix':
dir_path = '/tmp'
else:
dir_path = '.'
prefix = readMRtrixConfSetting('TmpFilePrefix')
if not prefix:
prefix = os.path.basename(sys.argv[0]) + '-tmp-'
tempDir = dir_path
while os.path.isdir(tempDir):
random_string = ''.join(random.choice(string.ascii_uppercase + string.digits) for x in range(6))
tempDir = os.path.join(dir_path, prefix + random_string) + os.sep
os.makedirs(tempDir)
printMessage('Generated temporary directory: ' + tempDir)
with open(os.path.join(tempDir, 'cwd.txt'), 'w') as outfile:
outfile.write(workingDir + '\n')
with open(os.path.join(tempDir, 'command.txt'), 'w') as outfile:
outfile.write(' '.join(sys.argv) + '\n')
def moveFileToDest(local_path, destination):
import os, shutil
from lib.printMessage import printMessage
if destination[0] != '/':
destination = os.path.abspath(os.path.join(workingDir, destination))
printMessage('Moving output file from temporary directory to user specified location')
shutil.move(local_path, destination)
def delFile(path):
import lib.app, os
from lib.printMessage import printMessage
if not lib.app.cleanup:
return
printMessage('Deleting file: ' + path)
os.remove(path)
def gotoTempDir():
import os
from lib.printMessage import printMessage
if verbosity:
printMessage("Changing to temporary directory (" + tempDir + ")")
os.chdir(tempDir)
def initialise():
import argparse, os, random, string, sys
from lib.printMessage import printMessage
from lib.readMRtrixConfSetting import readMRtrixConfSetting
global args, cleanup, lastFile, mrtrixNThreads, mrtrixQuiet, tempDir, verbosity, workingDir
global colourClear, colourConsole, colourError, colourPrint, colourWarn
workingDir = os.getcwd()
args = parser.parse_args()
if args.nocleanup:
cleanup = False
if args.nthreads:
mrtrixNThreads = "-nthreads " + args.nthreads
if args.quiet:
verbosity = 0
mrtrixQuiet = "-quiet"
if args.verbose:
verbosity = 2
mrtrixQuiet = ""
if args.cont:
tempDir = os.path.abspath(args.cont[0])
lastFile = args.cont[1]
else:
if args.tempdir:
dir_path = os.path.abspath(args.tempdir)
else:
dir_path = readMRtrixConfSetting("TmpFileDir")
if not dir_path:
if os.name == "posix":
dir_path = "/tmp"
else:
dir_path = "."
prefix = readMRtrixConfSetting("TmpFilePrefix")
if not prefix:
prefix = os.path.basename(sys.argv[0]) + "-tmp-"
tempDir = dir_path
while os.path.isdir(tempDir):
random_string = "".join(random.choice(string.ascii_uppercase + string.digits) for x in range(6))
tempDir = os.path.join(dir_path, prefix + random_string) + os.sep
os.makedirs(tempDir)
printMessage("Generated temporary directory: " + tempDir)
with open(os.path.join(tempDir, "cwd.txt"), "w") as outfile:
outfile.write(workingDir + "\n")
with open(os.path.join(tempDir, "command.txt"), "w") as outfile:
outfile.write(" ".join(sys.argv) + "\n")
use_colour = readMRtrixConfSetting("TerminalColor")
if use_colour:
use_colour = use_colour.lower() in ("yes", "true", "1")
else:
use_colour = not sys.platform.startswith("win")
if use_colour:
colourClear = "\033[0m"
colourConsole = "\033[03;34m"
colourError = "\033[01;31m"
colourPrint = "\033[03;32m"
colourWarn = "\033[00;31m"
def gotoTempDir():
import os
from lib.errorMessage import errorMessage
from lib.printMessage import printMessage
global tempDir
if not tempDir:
errorMessage('Script error: No temporary directory location set')
if verbosity:
printMessage('Changing to temporary directory (' + tempDir + ')')
os.chdir(tempDir)
def gotoTempDir():
import os
from lib.errorMessage import errorMessage
from lib.printMessage import printMessage
global tempDir
if not tempDir:
errorMessage('Script error: No temporary directory location set')
if verbosity:
printMessage('Changing to temporary directory (' + tempDir + ')')
os.chdir(tempDir)
def getHeaderInfo(image_path, header_item):
import lib.app, os, subprocess, sys
from lib.printMessage import printMessage
command = 'mrinfo ' + image_path + ' -' + header_item
if lib.app.verbosity > 1:
printMessage('Command: \'' + command + '\' (piping data to local storage)')
proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=None, shell=True)
result = proc.stdout.read()
result = result.rstrip().decode('utf-8')
if lib.app.verbosity > 1:
printMessage ('Result: ' + result)
return result
def complete():
import os, shutil, sys
from lib.printMessage import printMessage
printMessage('Changing back to original directory (' + workingDir + ')')
os.chdir(workingDir)
if cleanup:
printMessage('Deleting temporary directory ' + tempDir)
shutil.rmtree(tempDir)
else:
# This needs to be printed even if the -quiet option is used
sys.stdout.write(os.path.basename(sys.argv[0]) + ': ' + colourPrint + 'Contents of temporary directory kept, location: ' + tempDir + colourClear + '\n')
sys.stdout.flush()
def complete():
import os, shutil, sys
from lib.printMessage import printMessage
printMessage('Changing back to original directory (' + workingDir + ')')
os.chdir(workingDir)
if cleanup:
printMessage('Deleting temporary directory ' + tempDir)
shutil.rmtree(tempDir)
else:
# This needs to be printed even if the -quiet option is used
sys.stdout.write(os.path.basename(sys.argv[0]) + ': ' + colourPrint + 'Contents of temporary directory kept, location: ' + tempDir + colourClear + '\n')
sys.stdout.flush()
def getHeaderInfo(image_path, header_item):
import lib.app, subprocess
from lib.printMessage import printMessage
command = [ 'mrinfo', image_path, '-' + header_item ]
if lib.app.verbosity > 1:
printMessage('Command: \'' + ' '.join(command) + '\' (piping data to local storage)')
proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=None)
result, err = proc.communicate()
result = result.rstrip().decode('utf-8')
if lib.app.verbosity > 1:
printMessage('Result: ' + result)
return result
def getHeaderInfo(image_path, header_item):
import lib.app, subprocess
from lib.printMessage import printMessage
command = ['mrinfo', image_path, '-' + header_item]
if lib.app.verbosity > 1:
printMessage('Command: \'' + ' '.join(command) +
'\' (piping data to local storage)')
proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=None)
result, err = proc.communicate()
result = result.rstrip().decode('utf-8')
if lib.app.verbosity > 1:
printMessage('Result: ' + result)
return result
def getImageStat(image_path, statistic, mask_path = ''):
import lib.app, os, subprocess, sys
from lib.printMessage import printMessage
command = 'mrstats ' + image_path + ' -output ' + statistic
if mask_path:
command += ' -mask ' + mask_path
if lib.app.verbosity > 1:
printMessage('Command: \'' + command + '\' (piping data to local storage)')
proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=None, shell=True)
result = proc.stdout.read()
result = result.rstrip().decode('utf-8')
if lib.app.verbosity > 1:
printMessage('Result: ' + result)
return result
def getImageStat(image_path, statistic, mask_path=''):
import lib.app, subprocess
from lib.printMessage import printMessage
command = ['mrstats', image_path, '-output', statistic]
if mask_path:
command.extend(['-mask', mask_path])
if lib.app.verbosity > 1:
printMessage('Command: \'' + ' '.join(command) +
'\' (piping data to local storage)')
proc = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=None)
result, err = proc.communicate()
result = result.rstrip().decode('utf-8')
if lib.app.verbosity > 1:
printMessage('Result: ' + result)
return result
def getHeaderInfo(image_path, header_item):
import lib.app, os, subprocess, sys
from lib.printMessage import printMessage
command = 'mrinfo ' + image_path + ' -' + header_item
if lib.app.verbosity > 1:
printMessage('Command: \'' + command +
'\' (piping data to local storage)')
proc = subprocess.Popen(command,
stdout=subprocess.PIPE,
stderr=None,
shell=True)
result = proc.stdout.read()
result = result.rstrip().decode('utf-8')
if lib.app.verbosity > 1:
printMessage('Result: ' + result)
return result
def initialise(n):
import os, random, string, sys
from lib.printMessage import printMessage
from lib.readMRtrixConfSetting import readMRtrixConfSetting
global cleanup, mrtrixQuiet, numArgs, tempDir, verbosity, workingDir
#if not numArgs:
# sys.stderr.write('Must set numArgs value before calling initialise()\n')
# exit(1)
numArgs = n
workingDir = os.getcwd()
for option in sys.argv[numArgs+1:]:
if '-verbose'.startswith(option):
verbosity = 2
mrtrixQuiet = ''
elif '-quiet'.startswith(option):
verbosity = 0
mrtrixQuiet = '-quiet'
elif '-nocleanup'.startswith(option):
cleanup = False
else:
sys.stderr.write('Unknown option: ' + option + '\n')
exit(1)
# Create the temporary directory
dir_path = readMRtrixConfSetting('TmpFileDir')
if not dir_path:
if os.name == 'posix':
dir_path = '/tmp'
else:
dir_path = '.'
prefix = readMRtrixConfSetting('TmpFilePrefix')
if not prefix:
prefix = os.path.basename(sys.argv[0]) + '-tmp-'
tempDir = dir_path
while os.path.isdir(tempDir):
random_string = ''.join(random.choice(string.ascii_uppercase + string.digits) for x in range(6))
tempDir = os.path.join(dir_path, prefix + random_string) + os.sep
os.makedirs(tempDir)
printMessage('Generated temporary directory: ' + tempDir)
def makeTempDir():
import os, random, string, sys
from lib.errorMessage import errorMessage
from lib.printMessage import printMessage
from lib.readMRtrixConfSetting import readMRtrixConfSetting
global args, tempDir
if args.cont:
printMessage(
'Skipping temporary directory creation due to use of -continue option'
)
return
if tempDir:
errorMessage('Script error: Cannot use multiple temporary directories')
if args.tempdir:
dir_path = os.path.abspath(args.tempdir)
else:
dir_path = readMRtrixConfSetting('TmpFileDir')
if not dir_path:
if os.name == 'posix':
dir_path = '/tmp'
else:
dir_path = '.'
prefix = readMRtrixConfSetting('TmpFilePrefix')
if not prefix:
prefix = os.path.basename(sys.argv[0]) + '-tmp-'
tempDir = dir_path
while os.path.isdir(tempDir):
random_string = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for x in range(6))
tempDir = os.path.join(dir_path, prefix + random_string) + os.sep
os.makedirs(tempDir)
printMessage('Generated temporary directory: ' + tempDir)
with open(os.path.join(tempDir, 'cwd.txt'), 'w') as outfile:
outfile.write(workingDir + '\n')
with open(os.path.join(tempDir, 'command.txt'), 'w') as outfile:
outfile.write(' '.join(sys.argv) + '\n')
def terminate():
import os, shutil
from lib.printMessage import printMessage
printMessage('Changing back to original directory (' + workingDir + ')')
os.chdir(workingDir)
if cleanup:
printMessage('Deleting temporary directory ' + tempDir)
shutil.rmtree(tempDir)
else:
printMessage('Contents of temporary directory kept, location: ' + tempDir)
lib.app.makeTempDir()
# read in group subset if supplied
subset = []
if lib.app.args.group_subset:
subset = lib.app.args.group_subset[0].split(',')
# running participant level 1 (basic preprocessing)
if lib.app.args.analysis_level == 'participant1':
subprocess.check_call('bids-validator ' + lib.app.args.bids_dir, shell=True)
for subject_label in subjects_to_analyze:
label = 'sub-' + subject_label
printMessage('running basic pre-processing for ' + label)
# Read DWI(s) in BIDS folder
all_dwi_images = glob(os.path.join(lib.app.args.bids_dir, label, '*dwi', '*_dwi.nii*'))
# TODO handle multiple DWIs (e.g. time points) in subject directory
if (len(all_dwi_images) > 1):
errorMessage('Multiple DWIs found in subject folder. Multiple sessions not currently supported.')
# Create output subject directory
subject_dir = os.path.join(all_subjects_dir, subject_label)
if not os.path.exists(subject_dir):
os.mkdir(subject_dir)
# Check existence output files from this analysis level
dwi_preproc_file = os.path.join(subject_dir, 'dwi_preproc.mif')
def initialise():
import argparse, os, random, string, sys
from lib.printMessage import printMessage
from lib.printUsageMarkdown import printUsageMarkdown
from lib.printUsageRst import printUsageRst
from lib.readMRtrixConfSetting import readMRtrixConfSetting
global args, author, cleanup, lastFile, mrtrixNThreads, mrtrixQuiet, standardOptions, parser, refList, tempDir, verbosity, workingDir
global colourClear, colourConsole, colourError, colourPrint, colourWarn
if len(sys.argv) == 2 and sys.argv[1] == '__print_usage_markdown__':
printUsageMarkdown(parser, standardOptions, refList, author)
exit(0)
if len(sys.argv) == 2 and sys.argv[1] == '__print_usage_rst__':
printUsageRst(parser, standardOptions, refList, author)
exit(0)
workingDir = os.getcwd()
args = parser.parse_args()
if args.help or len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
use_colour = readMRtrixConfSetting('TerminalColor')
if use_colour:
use_colour = use_colour.lower() in ('yes', 'true', '1')
else:
use_colour = not sys.platform.startswith('win')
if use_colour:
colourClear = '\033[0m'
colourConsole = '\033[03;34m'
colourError = '\033[01;31m'
colourPrint = '\033[03;32m'
colourWarn = '\033[00;31m'
if args.nocleanup:
cleanup = False
if args.nthreads:
mrtrixNThreads = ' -nthreads ' + args.nthreads
if args.quiet:
verbosity = 0
mrtrixQuiet = ' -quiet'
if args.verbose:
verbosity = 2
mrtrixQuiet = ''
if citationWarning:
printMessage('')
printMessage(citationWarning)
printMessage('')
if args.cont:
tempDir = os.path.abspath(args.cont[0])
lastFile = args.cont[1]
else:
if args.tempdir:
dir_path = os.path.abspath(args.tempdir)
else:
dir_path = readMRtrixConfSetting('TmpFileDir')
if not dir_path:
if os.name == 'posix':
dir_path = '/tmp'
else:
dir_path = '.'
prefix = readMRtrixConfSetting('TmpFilePrefix')
if not prefix:
prefix = os.path.basename(sys.argv[0]) + '-tmp-'
tempDir = dir_path
while os.path.isdir(tempDir):
random_string = ''.join(random.choice(string.ascii_uppercase + string.digits) for x in range(6))
tempDir = os.path.join(dir_path, prefix + random_string) + os.sep
os.makedirs(tempDir)
printMessage('Generated temporary directory: ' + tempDir)
with open(os.path.join(tempDir, 'cwd.txt'), 'w') as outfile:
outfile.write(workingDir + '\n')
with open(os.path.join(tempDir, 'command.txt'), 'w') as outfile:
outfile.write(' '.join(sys.argv) + '\n')
def execute():
import math, os, shutil
import lib.app
from lib.getHeaderInfo import getHeaderInfo
from lib.getImageStat import getImageStat
from lib.getUserPath import getUserPath
from lib.printMessage import printMessage
from lib.runCommand import runCommand
from lib.warnMessage import warnMessage
from lib.errorMessage import errorMessage
# 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
sizes = [ int(x) for x in getHeaderInfo('5tt.mif', 'size').split() ]
datatype = getHeaderInfo('5tt.mif', 'datatype')
if not len(sizes) == 4 or not sizes[3] == 5 or not datatype.startswith('Float'):
errorMessage('Imported anatomical image ' + os.path.basename(lib.app.args.in_5tt) + ' is not in the 5TT format')
# Get shell information
shells = [ int(round(float(x))) for x in getHeaderInfo('dwi.mif', 'shells').split() ]
if len(shells) < 3:
warnMessage('Less than three b-value shells; response functions will not be applicable in MSMT-CSD algorithm')
# Get lmax information (if provided)
wm_lmax = [ ]
if lib.app.args.lmax:
wm_lmax = [ int(x.strip()) for x in lib.app.args.lmax.split(',') ]
if not len(wm_lmax) == len(shells):
errorMessage('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:
errorMessage('Values for lmax must be even')
if l<0:
errorMessage('Values for lmax must be non-negative')
runCommand('dwi2tensor dwi.mif - -mask mask.mif | tensor2metric - -fa fa.mif -vector vector.mif')
if not os.path.exists('dirs.mif'):
shutil.copy('vector.mif', 'dirs.mif')
runCommand('mrtransform 5tt.mif 5tt_regrid.mif -template fa.mif -interp linear')
# Basic tissue masks
runCommand('mrconvert 5tt_regrid.mif - -coord 3 2 -axes 0,1,2 | mrcalc - ' + str(lib.app.args.pvf) + ' -gt mask.mif -mult wm_mask.mif')
runCommand('mrconvert 5tt_regrid.mif - -coord 3 0 -axes 0,1,2 | mrcalc - ' + str(lib.app.args.pvf) + ' -gt fa.mif ' + str(lib.app.args.fa) + ' -lt -mult mask.mif -mult gm_mask.mif')
runCommand('mrconvert 5tt_regrid.mif - -coord 3 3 -axes 0,1,2 | mrcalc - ' + str(lib.app.args.pvf) + ' -gt fa.mif ' + str(lib.app.args.fa) + ' -lt -mult mask.mif -mult csf_mask.mif')
# Revise WM mask to only include single-fibre voxels
printMessage('Calling dwi2response recursively to select WM single-fibre voxels using \'' + lib.app.args.wm_algo + '\' algorithm')
recursive_cleanup_option=''
if not lib.app.cleanup:
recursive_cleanup_option = ' -nocleanup'
runCommand('dwi2response -quiet -tempdir ' + lib.app.tempDir + recursive_cleanup_option + ' ' + lib.app.args.wm_algo + ' dwi.mif wm_ss_response.txt -mask wm_mask.mif -voxels wm_sf_mask.mif')
# Check for empty masks
wm_voxels = int(getImageStat('wm_sf_mask.mif', 'count', 'wm_sf_mask.mif'))
gm_voxels = int(getImageStat('gm_mask.mif', 'count', 'gm_mask.mif'))
csf_voxels = int(getImageStat('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'
errorMessage(message)
# For each of the three tissues, generate a multi-shell response
# Since here we're guaranteeing that GM and CSF will be isotropic in all shells, let's use mrstats rather than sh2response (seems a bit weird passing a directions file to sh2response with lmax=0...)
wm_responses = [ ]
gm_responses = [ ]
csf_responses = [ ]
max_length = 0
for index, b in enumerate(shells):
dwi_path = 'dwi_b' + str(b) + '.mif'
# dwiextract will yield a 4D image, even if there's only a single volume in a shell
runCommand('dwiextract dwi.mif -shell ' + str(b) + ' ' + dwi_path)
this_b_lmax_option = ''
if wm_lmax:
this_b_lmax_option = ' -lmax ' + str(wm_lmax[index])
runCommand('amp2sh ' + dwi_path + ' - | sh2response - wm_sf_mask.mif dirs.mif wm_response_b' + str(b) + '.txt' + this_b_lmax_option)
wm_response = open('wm_response_b' + str(b) + '.txt', 'r').read().split()
wm_responses.append(wm_response)
max_length = max(max_length, len(wm_response))
mean_dwi_path = 'dwi_b' + str(b) + '_mean.mif'
runCommand('mrmath ' + dwi_path + ' mean ' + mean_dwi_path + ' -axis 3')
gm_mean = float(getImageStat(mean_dwi_path, 'mean', 'gm_mask.mif'))
csf_mean = float(getImageStat(mean_dwi_path, 'mean', 'csf_mask.mif'))
gm_responses .append( str(gm_mean * math.sqrt(4.0 * math.pi)) )
csf_responses.append( str(csf_mean * math.sqrt(4.0 * math.pi)) )
with open('wm.txt', 'w') as f:
for line in wm_responses:
line += ['0'] * (max_length - len(line))
f.write(' '.join(line) + '\n')
with open('gm.txt', 'w') as f:
for line in gm_responses:
f.write(line + '\n')
with open('csf.txt', 'w') as f:
for line in csf_responses:
f.write(line + '\n')
shutil.copyfile('wm.txt', getUserPath(lib.app.args.out_wm, False))
shutil.copyfile('gm.txt', getUserPath(lib.app.args.out_gm, False))
shutil.copyfile('csf.txt', getUserPath(lib.app.args.out_csf, False))
# Generate output 4D binary image with voxel selections; RGB as in MSMT-CSD paper
runCommand('mrcat csf_mask.mif gm_mask.mif wm_sf_mask.mif voxels.mif -axis 3')
lib.app.makeTempDir()
# read in group subset if supplied
subset = []
if lib.app.args.group_subset:
subset = lib.app.args.group_subset[0].split(',')
# running participant level 1 (calculate response function )
if lib.app.args.analysis_level == 'participant1':
for subject_label in subjects_to_analyze:
label = 'sub-' + subject_label
printMessage('running pre-processing for ' + label)
# Read DWI in BIDS derivatives folder
all_dwi_images = glob(os.path.join(lib.app.args.bids_dir, label, '*dwi', '*_dwi.nii*'))
# Create output subject directory
subject_dir = os.path.join(all_subjects_dir, subject_label)
if not os.path.exists(subject_dir):
os.mkdir(subject_dir)
# Check existence output files from this analysis level
dwi_preproc_file = os.path.join(subject_dir, 'dwi_preproc.mif')
lib.app.checkOutputFile(dwi_preproc_file)
wm_response_file = os.path.join(subject_dir, 'wm_response.txt')
lib.app.checkOutputFile(wm_response_file)
def execute():
import os, shutil
import lib.app
from lib.delFile import delFile
from lib.getImageStat import getImageStat
from lib.getUserPath import getUserPath
from lib.printMessage import printMessage
from lib.runCommand import runCommand
lmax_option = ''
if lib.app.args.lmax:
lmax_option = ' -lmax ' + lib.app.args.lmax
if lib.app.args.max_iters < 2:
errorMessage('Number of iterations must be at least 2')
runCommand('amp2sh dwi.mif dwiSH.mif' + lmax_option)
for iteration in range(0, lib.app.args.max_iters):
prefix = 'iter' + str(iteration) + '_'
if iteration == 0:
RF_in_path = 'init_RF.txt'
mask_in_path = 'mask.mif'
init_RF = '1 -1 1'
with open(RF_in_path, 'w') as f:
f.write(init_RF);
iter_lmax_option = ' -lmax 4'
else:
RF_in_path = 'iter' + str(iteration-1) + '_RF.txt'
mask_in_path = 'iter' + str(iteration-1) + '_SF_dilated.mif'
iter_lmax_option = lmax_option
# Run CSD
runCommand('dwi2fod csd dwi.mif ' + RF_in_path + ' ' + prefix + 'FOD.mif -mask ' + mask_in_path + iter_lmax_option)
# Get amplitudes of two largest peaks, and direction of largest
# TODO Speed-test fod2fixel against sh2peaks
# TODO Add maximum number of fixels per voxel option to fod2fixel?
runCommand('fod2fixel ' + prefix + 'FOD.mif -peak ' + prefix + 'peaks.msf -mask ' + mask_in_path + ' -fmls_no_thresholds')
delFile(prefix + 'FOD.mif')
if iteration:
delFile(mask_in_path)
runCommand('fixel2voxel ' + prefix + 'peaks.msf split_value ' + prefix + 'amps.mif')
runCommand('mrconvert ' + prefix + 'amps.mif ' + prefix + 'first_peaks.mif -coord 3 0 -axes 0,1,2')
runCommand('mrconvert ' + prefix + 'amps.mif ' + prefix + 'second_peaks.mif -coord 3 1 -axes 0,1,2')
delFile(prefix + 'amps.mif')
runCommand('fixel2voxel ' + prefix + 'peaks.msf split_dir ' + prefix + 'all_dirs.mif')
delFile(prefix + 'peaks.msf')
runCommand('mrconvert ' + prefix + 'all_dirs.mif ' + prefix + 'first_dir.mif -coord 3 0:2')
delFile(prefix + 'all_dirs.mif')
# Calculate the 'cost function' Donald derived for selecting single-fibre voxels
# https://github.com/MRtrix3/mrtrix3/pull/426
# sqrt(|peak1|) * (1 - |peak2| / |peak1|)^2
runCommand('mrcalc ' + prefix + 'first_peaks.mif -sqrt 1 ' + prefix + 'second_peaks.mif ' + prefix + 'first_peaks.mif -div -sub 2 -pow -mult '+ prefix + 'CF.mif')
delFile(prefix + 'first_peaks.mif')
delFile(prefix + 'second_peaks.mif')
# Select the top-ranked voxels
runCommand('mrthreshold ' + prefix + 'CF.mif -top ' + str(lib.app.args.sf_voxels) + ' ' + prefix + 'SF.mif')
# Generate a new response function based on this selection
runCommand('sh2response dwiSH.mif ' + prefix + 'SF.mif ' + prefix + 'first_dir.mif ' + prefix + 'RF.txt' + iter_lmax_option)
delFile(prefix + 'first_dir.mif')
# Should we terminate?
if iteration > 0:
runCommand('mrcalc ' + prefix + 'SF.mif iter' + str(iteration-1) + '_SF.mif -sub ' + prefix + 'SF_diff.mif')
delFile('iter' + str(iteration-1) + '_SF.mif')
max_diff = getImageStat(prefix + 'SF_diff.mif', 'max')
delFile(prefix + 'SF_diff.mif')
if int(max_diff) == 0:
printMessage('Convergence of SF voxel selection detected at iteration ' + str(iteration))
delFile(prefix + 'CF.mif')
shutil.copyfile(prefix + 'RF.txt', 'response.txt')
shutil.move(prefix + 'SF.mif', 'voxels.mif')
break
# Select a greater number of top single-fibre voxels, and dilate (within bounds of initial mask);
# these are the voxels that will be re-tested in the next iteration
runCommand('mrthreshold ' + prefix + 'CF.mif -top ' + str(lib.app.args.iter_voxels) + ' - | maskfilter - dilate - -npass ' + str(lib.app.args.dilate) + ' | mrcalc mask.mif - -mult ' + prefix + 'SF_dilated.mif')
delFile(prefix + 'CF.mif')
# Commence the next iteration
# If terminating due to running out of iterations, still need to put the results in the appropriate location
if not os.path.exists('response.txt'):
printMessage('Exiting after maximum ' + str(lib.app.args.max_iters) + ' iterations')
shutil.copyfile('iter' + str(lib.app.args.max_iters-1) + '_RF.txt', 'response.txt')
shutil.move('iter' + str(lib.app.args.max_iters-1) + '_SF.mif', 'voxels.mif')
shutil.copyfile('response.txt', getUserPath(lib.app.args.output, False))
def runCommand(cmd, exitOnError=True):
import lib.app, os, subprocess, sys
from lib.errorMessage import errorMessage
from lib.isWindows import isWindows
from lib.printMessage import printMessage
from lib.warnMessage import warnMessage
import distutils
from distutils.spawn import find_executable
global mrtrix_bin_list
global mrtrix_bin_path
if not mrtrix_bin_list:
mrtrix_bin_path = os.path.abspath(os.path.join(os.path.abspath(os.path.dirname(os.path.realpath(__file__))), os.pardir, os.pardir, 'release', 'bin'));
# On Windows, strip the .exe's
mrtrix_bin_list = [ os.path.splitext(name)[0] for name in os.listdir(mrtrix_bin_path) ]
if lib.app.lastFile:
# Check to see if the last file produced is produced by this command;
# if it is, this will be the last called command that gets skipped
if lib.app.lastFile in cmd:
lib.app.lastFile = ''
if lib.app.verbosity:
sys.stdout.write('Skipping command: ' + cmd + '\n')
sys.stdout.flush()
return
# Vectorise the command string, preserving anything encased within quotation marks
# This will eventually allow the use of subprocess rather than os.system()
# TODO Use shlex.split()?
quotation_split = cmd.split('\"')
if not len(quotation_split)%2:
errorMessage('Malformed command \"' + cmd + '\": odd number of quotation marks')
cmdsplit = [ ]
if len(quotation_split) == 1:
cmdsplit = cmd.split()
else:
for index, item in enumerate(quotation_split):
if index%2:
cmdsplit.append(item)
else:
cmdsplit.extend(item.split())
# For any MRtrix commands, need to insert the nthreads and quiet calls
new_cmdsplit = [ ]
is_mrtrix_binary = False
next_is_binary = True
for item in cmdsplit:
if next_is_binary:
is_mrtrix_binary = item in mrtrix_bin_list
# Make sure we're not accidentally running an MRtrix command from a different installation to the script
if is_mrtrix_binary:
binary_sys = find_executable(item)
binary_manual = os.path.join(mrtrix_bin_path, item)
if (isWindows()):
binary_manual = binary_manual + '.exe'
use_manual_binary_path = not binary_sys
if not use_manual_binary_path:
# os.path.samefile() not supported on all platforms / Python versions
if hasattr(os.path, 'samefile'):
use_manual_binary_path = not os.path.samefile(binary_sys, binary_manual)
else:
# Hack equivalent of samefile(); not perfect, but should be adequate for use here
use_manual_binary_path = not os.path.normcase(os.path.normpath(binary_sys)) == os.path.normcase(os.path.normpath(binary_manual))
if use_manual_binary_path:
item = binary_manual
next_is_binary = False
if item == '|':
if is_mrtrix_binary:
if lib.app.mrtrixNThreads:
new_cmdsplit.extend(lib.app.mrtrixNThreads.strip().split())
if lib.app.mrtrixQuiet:
new_cmdsplit.append(lib.app.mrtrixQuiet.strip())
next_is_binary = True
new_cmdsplit.append(item)
if is_mrtrix_binary:
if lib.app.mrtrixNThreads:
new_cmdsplit.extend(lib.app.mrtrixNThreads.strip().split())
if lib.app.mrtrixQuiet:
new_cmdsplit.append(lib.app.mrtrixQuiet.strip())
cmdsplit = new_cmdsplit
# If the piping symbol appears anywhere, we need to split this into multiple commands and execute them separately
# If no piping symbols, the entire command should just appear as a single row in cmdstack
cmdstack = [ ]
prev = 0
for index, item in enumerate(cmdsplit):
if item == '|':
cmdstack.append(cmdsplit[prev:index])
prev = index + 1
cmdstack.append(cmdsplit[prev:])
if lib.app.verbosity:
sys.stdout.write(lib.app.colourConsole + 'Command:' + lib.app.colourClear + ' ' + cmd + '\n')
sys.stdout.flush()
error = False
error_text = ''
# TODO If script is running in verbose mode, ideally want to duplicate stderr output in the terminal
if len(cmdstack) == 1:
process = subprocess.Popen(cmdstack[0], stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
(stdoutdata, stderrdata) = process.communicate()
if process.returncode:
error = True
error_text = stdoutdata.decode('utf-8') + stderrdata.decode('utf-8')
else:
processes = [ ]
for index, command in enumerate(cmdstack):
if index > 0:
proc_in = processes[index-1].stdout
else:
proc_in = None
process = subprocess.Popen (command, stdin=proc_in, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
processes.append(process)
# Wait for all commands to complete
for index, process in enumerate(processes):
if index < len(cmdstack)-1:
# Only capture the output if the command failed; otherwise, let it pipe to the next command
process.wait()
if process.returncode:
error = True
(stdoutdata, stderrdata) = process.communicate()
error_text = error_text + stdoutdata.decode('utf-8') + stderrdata.decode('utf-8')
else:
(stdoutdata, stderrdata) = process.communicate()
if process.returncode:
error = True
error_text = error_text + stdoutdata.decode('utf-8') + stderrdata.decode('utf-8')
if (error):
if exitOnError:
printMessage('')
sys.stderr.write(os.path.basename(sys.argv[0]) + ': ' + lib.app.colourError + '[ERROR] Command failed: ' + cmd + lib.app.colourClear + '\n')
sys.stderr.write(os.path.basename(sys.argv[0]) + ': ' + lib.app.colourPrint + 'Output of failed command:' + lib.app.colourClear + '\n')
sys.stderr.write(error_text)
if not lib.app.cleanup and lib.app.tempDir:
with open(os.path.join(lib.app.tempDir, 'error.txt'), 'w') as outfile:
outfile.write(cmd + '\n\n' + error_text + '\n')
lib.app.complete()
exit(1)
else:
warnMessage('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 runCommand():
# other flags may potentially change if this file is eventually used to resume the script
if lib.app.tempDir:
with open(os.path.join(lib.app.tempDir, 'log.txt'), 'a') as outfile:
outfile.write(cmd + '\n')
def initialise():
import argparse, os, random, string, sys
from lib.printMessage import printMessage
from lib.printUsageMarkdown import printUsageMarkdown
from lib.printUsageRst import printUsageRst
from lib.readMRtrixConfSetting import readMRtrixConfSetting
global args, author, cleanup, lastFile, mrtrixNThreads, mrtrixQuiet, standardOptions, parser, refList, tempDir, verbosity, workingDir
global colourClear, colourConsole, colourError, colourPrint, colourWarn
if len(sys.argv) == 2 and sys.argv[1] == '__print_usage_markdown__':
printUsageMarkdown(parser, standardOptions, refList, author)
exit(0)
if len(sys.argv) == 2 and sys.argv[1] == '__print_usage_rst__':
printUsageRst(parser, standardOptions, refList, author)
exit(0)
workingDir = os.getcwd()
args = parser.parse_args()
if args.help or len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
use_colour = readMRtrixConfSetting('TerminalColor')
if use_colour:
use_colour = use_colour.lower() in ('yes', 'true', '1')
else:
use_colour = not sys.platform.startswith('win')
if use_colour:
colourClear = '\033[0m'
colourConsole = '\033[03;34m'
colourError = '\033[01;31m'
colourPrint = '\033[03;32m'
colourWarn = '\033[00;31m'
if args.nocleanup:
cleanup = False
if args.nthreads:
mrtrixNThreads = '-nthreads ' + args.nthreads
if args.quiet:
verbosity = 0
mrtrixQuiet = '-quiet'
if args.verbose:
verbosity = 2
mrtrixQuiet = ''
if citationWarning:
printMessage('')
printMessage(citationWarning)
printMessage('')
if args.cont:
tempDir = os.path.abspath(args.cont[0])
lastFile = args.cont[1]
else:
if args.tempdir:
dir_path = os.path.abspath(args.tempdir)
else:
dir_path = readMRtrixConfSetting('TmpFileDir')
if not dir_path:
if os.name == 'posix':
dir_path = '/tmp'
else:
dir_path = '.'
prefix = readMRtrixConfSetting('TmpFilePrefix')
if not prefix:
prefix = os.path.basename(sys.argv[0]) + '-tmp-'
tempDir = dir_path
while os.path.isdir(tempDir):
random_string = ''.join(
random.choice(string.ascii_uppercase + string.digits)
for x in range(6))
tempDir = os.path.join(dir_path, prefix + random_string) + os.sep
os.makedirs(tempDir)
printMessage('Generated temporary directory: ' + tempDir)
with open(os.path.join(tempDir, 'cwd.txt'), 'w') as outfile:
outfile.write(workingDir + '\n')
with open(os.path.join(tempDir, 'command.txt'), 'w') as outfile:
outfile.write(' '.join(sys.argv) + '\n')
def gotoTempDir():
import os
from lib.printMessage import printMessage
if verbosity:
printMessage('Changing to temporary directory (' + tempDir + ')')
os.chdir(tempDir)
def execute():
import math, os, shutil
import lib.app
from lib.getImageStat import getImageStat
from lib.getUserPath import getUserPath
from lib.printMessage import printMessage
from lib.runCommand import runCommand
lmax_option = ''
if lib.app.args.lmax:
lmax_option = ' -lmax ' + lib.app.args.lmax
runCommand('amp2sh dwi.mif dwiSH.mif' + lmax_option)
convergence_change = 0.01 * lib.app.args.convergence
for iteration in range(0, lib.app.args.max_iters):
prefix = 'iter' + str(iteration) + '_'
# How to initialise response function?
# old dwi2response command used mean & standard deviation of DWI data; however
# this may force the output FODs to lmax=2 at the first iteration
# Chantal used a tensor with low FA, but it'd be preferable to get the scaling right
# Other option is to do as before, but get the ratio between l=0 and l=2, and
# generate l=4,6,... using that amplitude ratio
if iteration == 0:
RF_in_path = 'init_RF.txt'
mask_in_path = 'mask.mif'
runCommand('dwiextract dwi.mif shell.mif')
# TODO This can be changed once #71 is implemented (mrstats statistics across volumes)
volume_means = [
float(x)
for x in getImageStat('shell.mif', 'mean', 'mask.mif').split()
]
mean = sum(volume_means) / float(len(volume_means))
volume_stds = [
float(x)
for x in getImageStat('shell.mif', 'std', 'mask.mif').split()
]
std = sum(volume_stds) / float(len(volume_stds))
# Scale these to reflect the fact that we're moving to the SH basis
mean *= math.sqrt(4.0 * math.pi)
std *= math.sqrt(4.0 * math.pi)
# Now produce the initial response function
# Let's only do it to lmax 4
init_RF = [
str(mean),
str(-0.5 * std),
str(0.25 * std * std / mean)
]
with open('init_RF.txt', 'w') as f:
f.write(' '.join(init_RF))
else:
RF_in_path = 'iter' + str(iteration - 1) + '_RF.txt'
mask_in_path = 'iter' + str(iteration - 1) + '_SF.mif'
# Run CSD
runCommand('dwi2fod csd dwi.mif ' + RF_in_path + ' ' + prefix +
'FOD.mif -mask ' + mask_in_path)
# Get amplitudes of two largest peaks, and directions of largest
runCommand('fod2fixel ' + prefix + 'FOD.mif -peak ' + prefix +
'peaks.msf -mask ' + mask_in_path + ' -fmls_no_thresholds')
runCommand('fixel2voxel ' + prefix + 'peaks.msf split_value ' +
prefix + 'amps.mif')
runCommand('mrconvert ' + prefix + 'amps.mif ' + prefix +
'first_peaks.mif -coord 3 0 -axes 0,1,2')
runCommand('mrconvert ' + prefix + 'amps.mif ' + prefix +
'second_peaks.mif -coord 3 1 -axes 0,1,2')
runCommand('fixel2voxel ' + prefix + 'peaks.msf split_dir ' + prefix +
'all_dirs.mif')
runCommand('mrconvert ' + prefix + 'all_dirs.mif ' + prefix +
'first_dir.mif -coord 3 0:2')
# Revise single-fibre voxel selection based on ratio of tallest to second-tallest peak
runCommand('mrcalc ' + prefix + 'second_peaks.mif ' + prefix +
'first_peaks.mif -div ' + prefix + 'peak_ratio.mif')
runCommand('mrcalc ' + prefix + 'peak_ratio.mif ' +
str(lib.app.args.peak_ratio) + ' -lt ' + mask_in_path +
' -mult ' + prefix + 'SF.mif')
# Make sure image isn't empty
SF_voxel_count = int(
getImageStat(prefix + 'SF.mif', 'count', prefix + 'SF.mif'))
if not SF_voxel_count:
errorMessage(
'Aborting: All voxels have been excluded from single-fibre selection'
)
# Generate a new response function
runCommand('sh2response dwiSH.mif ' + prefix + 'SF.mif ' + prefix +
'first_dir.mif ' + prefix + 'RF.txt' + lmax_option)
# Detect convergence
# Look for a change > some percentage - don't bother looking at the masks
if iteration > 0:
old_RF_file = open(RF_in_path, 'r')
old_RF = [float(x) for x in old_RF_file.read().split()]
new_RF_file = open(prefix + 'RF.txt', 'r')
new_RF = [float(x) for x in new_RF_file.read().split()]
reiterate = False
for index in range(0, len(old_RF)):
mean = 0.5 * (old_RF[index] + new_RF[index])
diff = math.fabs(0.5 * (old_RF[index] - new_RF[index]))
ratio = diff / mean
if ratio > convergence_change:
reiterate = True
if not reiterate:
printMessage(
'Exiting at iteration ' + str(iteration) + ' with ' +
str(SF_voxel_count) +
' SF voxels due to unchanged response function coefficients'
)
shutil.copyfile(prefix + 'RF.txt', 'response.txt')
shutil.copyfile(prefix + 'SF.mif', 'voxels.mif')
break
# Go to the next iteration
# If we've terminated due to hitting the iteration limiter, we still need to copy the output file(s) to the correct location
if not os.path.exists('response.txt'):
printMessage('Exiting after maximum ' +
str(lib.app.args.max_iters - 1) + ' iterations with ' +
str(SF_voxel_count) + ' SF voxels')
shutil.copyfile('iter' + str(lib.app.args.max_iters - 1) + '_RF.txt',
'response.txt')
shutil.copyfile('iter' + str(lib.app.args.max_iters - 1) + '_SF.mif',
'voxels.mif')
shutil.copyfile('response.txt', getUserPath(lib.app.args.output, False))
def initialise():
import os, sys
from lib.errorMessage import errorMessage
from lib.printMessage import printMessage
from lib.readMRtrixConfSetting import readMRtrixConfSetting
global args, citationList, cleanup, externalCitations, lastFile, mrtrixNThreads, mrtrixQuiet, parser, tempDir, verbosity, workingDir
global colourClear, colourConsole, colourError, colourPrint, colourWarn
if not parser:
errorMessage(
'Script error: Command-line parser must be initialised before app')
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
if sys.argv[-1] == '__print_usage_rst__':
parser.printUsageRst()
exit(0)
workingDir = os.getcwd()
args = parser.parse_args()
if args.help:
parser.print_help()
sys.exit(0)
use_colour = readMRtrixConfSetting('TerminalColor')
if use_colour:
use_colour = use_colour.lower() in ('yes', 'true', '1')
else:
# Windows now also gets coloured text terminal support, so make this the default
use_colour = True
if use_colour:
colourClear = '\033[0m'
colourConsole = '\033[03;34m'
colourError = '\033[01;31m'
colourPrint = '\033[03;32m'
colourWarn = '\033[00;31m'
if args.nocleanup:
cleanup = False
if args.nthreads:
mrtrixNThreads = ' -nthreads ' + args.nthreads
if args.quiet:
verbosity = 0
mrtrixQuiet = ' -quiet'
elif args.verbose:
verbosity = 2
mrtrixQuiet = ''
if citationList:
printMessage('')
citation_warning = 'Note that this script makes use of commands / algorithms that have relevant articles for citation'
if externalCitations:
citation_warning += '; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES'
citation_warning += '. Please consult the help page (-help option) for more information.'
printMessage(citation_warning)
printMessage('')
if args.cont:
tempDir = os.path.abspath(args.cont[0])
lastFile = args.cont[1]
def initialise():
import os, sys
from lib.errorMessage import errorMessage
from lib.printMessage import printMessage
from lib.readMRtrixConfSetting import readMRtrixConfSetting
global args, citationList, cleanup, externalCitations, lastFile, mrtrixNThreads, mrtrixQuiet, parser, tempDir, verbosity, workingDir
global colourClear, colourConsole, colourError, colourPrint, colourWarn
if not parser:
errorMessage('Script error: Command-line parser must be initialised before app')
if len(sys.argv) == 1:
parser.print_help()
sys.exit(0)
if sys.argv[-1] == '__print_usage_rst__':
parser.printUsageRst()
exit(0)
workingDir = os.getcwd()
args = parser.parse_args()
if args.help:
parser.print_help()
sys.exit(0)
use_colour = readMRtrixConfSetting('TerminalColor')
if use_colour:
use_colour = use_colour.lower() in ('yes', 'true', '1')
else:
# Windows now also gets coloured text terminal support, so make this the default
use_colour = True
if use_colour:
colourClear = '\033[0m'
colourConsole = '\033[03;34m'
colourError = '\033[01;31m'
colourPrint = '\033[03;32m'
colourWarn = '\033[00;31m'
if args.nocleanup:
cleanup = False
if args.nthreads:
mrtrixNThreads = ' -nthreads ' + args.nthreads
if args.quiet:
verbosity = 0
mrtrixQuiet = ' -quiet'
elif args.verbose:
verbosity = 2
mrtrixQuiet = ''
if citationList:
printMessage('')
citation_warning = 'Note that this script makes use of commands / algorithms that have relevant articles for citation'
if externalCitations:
citation_warning += '; INCLUDING FROM EXTERNAL SOFTWARE PACKAGES'
citation_warning += '. Please consult the help page (-help option) for more information.'
printMessage(citation_warning)
printMessage('')
if args.cont:
tempDir = os.path.abspath(args.cont[0])
lastFile = args.cont[1]
template_dir = os.path.join(lib.app.args.output_dir, 'template')
if not os.path.exists(template_dir):
os.mkdir(template_dir)
# create a temporary directory for intermediate files
lib.app.makeTempDir()
# read in group subset if supplied
subset = []
if lib.app.args.group_subset:
subset = lib.app.args.group_subset[0].split(',')
# running participant level 1 (coversion, mask, and bias correction )
if lib.app.args.analysis_level == 'participant1':
printMessage('performing intial conversion and bias correction')
for subject_label in subjects_to_analyze:
label = 'sub-' + subject_label
printMessage('running pre-processing for ' + label)
# Read DWI in BIDS derivatives folder
all_dwi_images = glob(
os.path.join(lib.app.args.bids_dir, label, '*dwi', '*_dwi.nii*'))
# Create output subject directory
subject_dir = os.path.join(all_subjects_dir, subject_label)
if not os.path.exists(subject_dir):
os.mkdir(subject_dir)
# Check existence output files from this analysis level
dwi_preproc_file = os.path.join(subject_dir, 'dwi_preproc.mif')
def execute():
import math, os, shutil
import lib.app
from lib.getHeaderInfo import getHeaderInfo
from lib.getImageStat import getImageStat
from lib.getUserPath import getUserPath
from lib.printMessage import printMessage
from lib.runCommand import runCommand
from lib.warnMessage import warnMessage
from lib.errorMessage import errorMessage
# 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
sizes = [int(x) for x in getHeaderInfo('5tt.mif', 'size').split()]
datatype = getHeaderInfo('5tt.mif', 'datatype')
if not len(sizes) == 4 or not sizes[3] == 5 or not datatype.startswith(
'Float'):
errorMessage('Imported anatomical image ' +
os.path.basename(lib.app.args.in_5tt) +
' is not in the 5TT format')
# Get shell information
shells = [
int(round(float(x)))
for x in getHeaderInfo('dwi.mif', 'shells').split()
]
if len(shells) < 3:
warnMessage(
'Less than three b-value shells; response functions will not be applicable in MSMT-CSD algorithm'
)
# Get lmax information (if provided)
wm_lmax = []
if lib.app.args.lmax:
wm_lmax = [int(x.strip()) for x in lib.app.args.lmax.split(',')]
if not len(wm_lmax) == len(shells):
errorMessage('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:
errorMessage('Values for lmax must be even')
if l < 0:
errorMessage('Values for lmax must be non-negative')
runCommand(
'dwi2tensor dwi.mif - -mask mask.mif | tensor2metric - -fa fa.mif -vector vector.mif'
)
if not os.path.exists('dirs.mif'):
shutil.copy('vector.mif', 'dirs.mif')
runCommand(
'mrtransform 5tt.mif 5tt_regrid.mif -template fa.mif -interp linear')
# Basic tissue masks
runCommand(
'mrconvert 5tt_regrid.mif - -coord 3 2 -axes 0,1,2 | mrcalc - ' +
str(lib.app.args.pvf) + ' -gt mask.mif -mult wm_mask.mif')
runCommand(
'mrconvert 5tt_regrid.mif - -coord 3 0 -axes 0,1,2 | mrcalc - ' +
str(lib.app.args.pvf) + ' -gt fa.mif ' + str(lib.app.args.fa) +
' -lt -mult mask.mif -mult gm_mask.mif')
runCommand(
'mrconvert 5tt_regrid.mif - -coord 3 3 -axes 0,1,2 | mrcalc - ' +
str(lib.app.args.pvf) + ' -gt fa.mif ' + str(lib.app.args.fa) +
' -lt -mult mask.mif -mult csf_mask.mif')
# Revise WM mask to only include single-fibre voxels
printMessage(
'Calling dwi2response recursively to select WM single-fibre voxels using \''
+ lib.app.args.wm_algo + '\' algorithm')
recursive_cleanup_option = ''
if not lib.app.cleanup:
recursive_cleanup_option = ' -nocleanup'
runCommand(
'dwi2response -quiet -tempdir ' + lib.app.tempDir +
recursive_cleanup_option + ' ' + lib.app.args.wm_algo +
' dwi.mif wm_ss_response.txt -mask wm_mask.mif -voxels wm_sf_mask.mif')
# Check for empty masks
wm_voxels = int(getImageStat('wm_sf_mask.mif', 'count', 'wm_sf_mask.mif'))
gm_voxels = int(getImageStat('gm_mask.mif', 'count', 'gm_mask.mif'))
csf_voxels = int(getImageStat('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'
errorMessage(message)
# For each of the three tissues, generate a multi-shell response
# Since here we're guaranteeing that GM and CSF will be isotropic in all shells, let's use mrstats rather than sh2response (seems a bit weird passing a directions file to sh2response with lmax=0...)
wm_responses = []
gm_responses = []
csf_responses = []
max_length = 0
for index, b in enumerate(shells):
dwi_path = 'dwi_b' + str(b) + '.mif'
# dwiextract will yield a 4D image, even if there's only a single volume in a shell
runCommand('dwiextract dwi.mif -shell ' + str(b) + ' ' + dwi_path)
this_b_lmax_option = ''
if wm_lmax:
this_b_lmax_option = ' -lmax ' + str(wm_lmax[index])
runCommand('amp2sh ' + dwi_path +
' - | sh2response - wm_sf_mask.mif dirs.mif wm_response_b' +
str(b) + '.txt' + this_b_lmax_option)
wm_response = open('wm_response_b' + str(b) + '.txt',
'r').read().split()
wm_responses.append(wm_response)
max_length = max(max_length, len(wm_response))
mean_dwi_path = 'dwi_b' + str(b) + '_mean.mif'
runCommand('mrmath ' + dwi_path + ' mean ' + mean_dwi_path +
' -axis 3')
gm_mean = float(getImageStat(mean_dwi_path, 'mean', 'gm_mask.mif'))
csf_mean = float(getImageStat(mean_dwi_path, 'mean', 'csf_mask.mif'))
gm_responses.append(str(gm_mean * math.sqrt(4.0 * math.pi)))
csf_responses.append(str(csf_mean * math.sqrt(4.0 * math.pi)))
with open('wm.txt', 'w') as f:
for line in wm_responses:
line += ['0'] * (max_length - len(line))
f.write(' '.join(line) + '\n')
with open('gm.txt', 'w') as f:
for line in gm_responses:
f.write(line + '\n')
with open('csf.txt', 'w') as f:
for line in csf_responses:
f.write(line + '\n')
shutil.copyfile('wm.txt', getUserPath(lib.app.args.out_wm, False))
shutil.copyfile('gm.txt', getUserPath(lib.app.args.out_gm, False))
shutil.copyfile('csf.txt', getUserPath(lib.app.args.out_csf, False))
# Generate output 4D binary image with voxel selections; RGB as in MSMT-CSD paper
runCommand(
'mrcat csf_mask.mif gm_mask.mif wm_sf_mask.mif voxels.mif -axis 3')
def runCommand(cmd, exitOnError=True):
import lib.app, os, subprocess, sys
from lib.errorMessage import errorMessage
from lib.isWindows import isWindows
from lib.printMessage import printMessage
from lib.warnMessage import warnMessage
import distutils
from distutils.spawn import find_executable
global mrtrix_bin_list
global mrtrix_bin_path
if not mrtrix_bin_list:
mrtrix_bin_path = os.path.abspath(
os.path.join(
os.path.abspath(os.path.dirname(os.path.realpath(__file__))),
os.pardir, os.pardir, 'release', 'bin'))
# On Windows, strip the .exe's
mrtrix_bin_list = [
os.path.splitext(name)[0] for name in os.listdir(mrtrix_bin_path)
]
if lib.app.lastFile:
# Check to see if the last file produced is produced by this command;
# if it is, this will be the last called command that gets skipped
if lib.app.lastFile in cmd:
lib.app.lastFile = ''
if lib.app.verbosity:
sys.stdout.write('Skipping command: ' + cmd + '\n')
sys.stdout.flush()
return
# Vectorise the command string, preserving anything encased within quotation marks
# This will eventually allow the use of subprocess rather than os.system()
# TODO Use shlex.split()?
quotation_split = cmd.split('\"')
if not len(quotation_split) % 2:
errorMessage('Malformed command \"' + cmd +
'\": odd number of quotation marks')
cmdsplit = []
if len(quotation_split) == 1:
cmdsplit = cmd.split()
else:
for index, item in enumerate(quotation_split):
if index % 2:
cmdsplit.append(item)
else:
cmdsplit.extend(item.split())
# For any MRtrix commands, need to insert the nthreads and quiet calls
new_cmdsplit = []
is_mrtrix_binary = False
next_is_binary = True
for item in cmdsplit:
if next_is_binary:
is_mrtrix_binary = item in mrtrix_bin_list
# Make sure we're not accidentally running an MRtrix command from a different installation to the script
if is_mrtrix_binary:
binary_sys = find_executable(item)
binary_manual = os.path.join(mrtrix_bin_path, item)
if (isWindows()):
binary_manual = binary_manual + '.exe'
use_manual_binary_path = not binary_sys
if not use_manual_binary_path:
# os.path.samefile() not supported on all platforms / Python versions
if hasattr(os.path, 'samefile'):
use_manual_binary_path = not os.path.samefile(
binary_sys, binary_manual)
else:
# Hack equivalent of samefile(); not perfect, but should be adequate for use here
use_manual_binary_path = not os.path.normcase(
os.path.normpath(binary_sys)) == os.path.normcase(
os.path.normpath(binary_manual))
if use_manual_binary_path:
item = binary_manual
next_is_binary = False
if item == '|':
if is_mrtrix_binary:
if lib.app.mrtrixNThreads:
new_cmdsplit.extend(lib.app.mrtrixNThreads.strip().split())
if lib.app.mrtrixQuiet:
new_cmdsplit.append(lib.app.mrtrixQuiet.strip())
next_is_binary = True
new_cmdsplit.append(item)
if is_mrtrix_binary:
if lib.app.mrtrixNThreads:
new_cmdsplit.extend(lib.app.mrtrixNThreads.strip().split())
if lib.app.mrtrixQuiet:
new_cmdsplit.append(lib.app.mrtrixQuiet.strip())
cmdsplit = new_cmdsplit
# If the piping symbol appears anywhere, we need to split this into multiple commands and execute them separately
# If no piping symbols, the entire command should just appear as a single row in cmdstack
cmdstack = []
prev = 0
for index, item in enumerate(cmdsplit):
if item == '|':
cmdstack.append(cmdsplit[prev:index])
prev = index + 1
cmdstack.append(cmdsplit[prev:])
if lib.app.verbosity:
sys.stdout.write(lib.app.colourConsole + 'Command:' +
lib.app.colourClear + ' ' + cmd + '\n')
sys.stdout.flush()
error = False
error_text = ''
# TODO If script is running in verbose mode, ideally want to duplicate stderr output in the terminal
if len(cmdstack) == 1:
process = subprocess.Popen(cmdstack[0],
stdin=None,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
(stdoutdata, stderrdata) = process.communicate()
if process.returncode:
error = True
error_text = stdoutdata.decode('utf-8') + stderrdata.decode(
'utf-8')
else:
processes = []
for index, command in enumerate(cmdstack):
if index > 0:
proc_in = processes[index - 1].stdout
else:
proc_in = None
process = subprocess.Popen(command,
stdin=proc_in,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
processes.append(process)
# Wait for all commands to complete
for index, process in enumerate(processes):
if index < len(cmdstack) - 1:
# Only capture the output if the command failed; otherwise, let it pipe to the next command
process.wait()
if process.returncode:
error = True
(stdoutdata, stderrdata) = process.communicate()
error_text = error_text + stdoutdata.decode(
'utf-8') + stderrdata.decode('utf-8')
else:
(stdoutdata, stderrdata) = process.communicate()
if process.returncode:
error = True
error_text = error_text + stdoutdata.decode(
'utf-8') + stderrdata.decode('utf-8')
if (error):
lib.app.cleanup = False
if exitOnError:
printMessage('')
sys.stderr.write(
os.path.basename(sys.argv[0]) + ': ' + lib.app.colourError +
'[ERROR] Command failed: ' + cmd + lib.app.colourClear + '\n')
sys.stderr.write(
os.path.basename(sys.argv[0]) + ': ' + lib.app.colourPrint +
'Output of failed command:' + lib.app.colourClear + '\n')
sys.stderr.write(error_text)
if lib.app.tempDir:
with open(os.path.join(lib.app.tempDir, 'error.txt'),
'w') as outfile:
outfile.write(cmd + '\n\n' + error_text + '\n')
lib.app.complete()
exit(1)
else:
warnMessage('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 runCommand():
# other flags may potentially change if this file is eventually used to resume the script
if lib.app.tempDir:
with open(os.path.join(lib.app.tempDir, 'log.txt'), 'a') as outfile:
outfile.write(cmd + '\n')
def execute():
import math, os, shutil
import lib.app
from lib.getImageStat import getImageStat
from lib.printMessage import printMessage
from lib.runCommand import runCommand
lmax_option = ''
if lib.app.args.lmax:
lmax_option = ' -lmax ' + lib.app.args.lmax
runCommand('amp2sh dwi.mif dwiSH.mif' + lmax_option)
convergence_change = 0.01 * lib.app.args.convergence
for iteration in range(0, lib.app.args.max_iters):
prefix = 'iter' + str(iteration) + '_'
# How to initialise response function?
# old dwi2response command used mean & standard deviation of DWI data; however
# this may force the output FODs to lmax=2 at the first iteration
# Chantal used a tensor with low FA, but it'd be preferable to get the scaling right
# Other option is to do as before, but get the ratio between l=0 and l=2, and
# generate l=4,6,... using that amplitude ratio
if iteration == 0:
RF_in_path = 'init_RF.txt'
mask_in_path = 'mask.mif'
runCommand('dwiextract dwi.mif shell.mif')
# TODO This can be changed once #71 is implemented (mrstats statistics across volumes)
volume_means = [float(x) for x in getImageStat('shell.mif', 'mean', 'mask.mif').split()]
mean = sum(volume_means) / float(len(volume_means))
volume_stds = [float(x) for x in getImageStat('shell.mif', 'std', 'mask.mif').split()]
std = sum(volume_stds) / float(len(volume_stds))
# Scale these to reflect the fact that we're moving to the SH basis
mean *= math.sqrt(4.0 * math.pi)
std *= math.sqrt(4.0 * math.pi)
# Now produce the initial response function
# Let's only do it to lmax 4
init_RF = [ str(mean), str(-0.5*std), str(0.25*std*std/mean) ]
with open('init_RF.txt', 'w') as f:
f.write(' '.join(init_RF))
else:
RF_in_path = 'iter' + str(iteration-1) + '_RF.txt'
mask_in_path = 'iter' + str(iteration-1) + '_SF.mif'
# Run CSD
runCommand('dwi2fod dwi.mif ' + RF_in_path + ' ' + prefix + 'FOD.mif -mask ' + mask_in_path)
# Get amplitudes of two largest peaks, and directions of largest
runCommand('fod2fixel ' + prefix + 'FOD.mif -peak ' + prefix + 'peaks.msf -mask ' + mask_in_path + ' -fmls_no_thresholds')
runCommand('fixel2voxel ' + prefix + 'peaks.msf split_value ' + prefix + 'amps.mif')
runCommand('mrconvert ' + prefix + 'amps.mif ' + prefix + 'first_peaks.mif -coord 3 0 -axes 0,1,2')
runCommand('mrconvert ' + prefix + 'amps.mif ' + prefix + 'second_peaks.mif -coord 3 1 -axes 0,1,2')
runCommand('fixel2voxel ' + prefix + 'peaks.msf split_dir ' + prefix + 'all_dirs.mif')
runCommand('mrconvert ' + prefix + 'all_dirs.mif ' + prefix + 'first_dir.mif -coord 3 0:2')
# Revise single-fibre voxel selection based on ratio of tallest to second-tallest peak
runCommand('mrcalc ' + prefix + 'second_peaks.mif ' + prefix + 'first_peaks.mif -div ' + prefix + 'peak_ratio.mif')
runCommand('mrcalc ' + prefix + 'peak_ratio.mif ' + str(lib.app.args.peak_ratio) + ' -lt ' + mask_in_path + ' -mult ' + prefix + 'SF.mif')
# Make sure image isn't empty
SF_voxel_count = int(getImageStat(prefix + 'SF.mif', 'count', prefix + 'SF.mif'))
if not SF_voxel_count:
errorMessage('Aborting: All voxels have been excluded from single-fibre selection')
# Generate a new response function
runCommand('sh2response dwiSH.mif ' + prefix + 'SF.mif ' + prefix + 'first_dir.mif ' + prefix + 'RF.txt' + lmax_option)
# Detect convergence
# Look for a change > some percentage - don't bother looking at the masks
if iteration > 0:
old_RF_file = open(RF_in_path, 'r')
old_RF = [ float(x) for x in old_RF_file.read().split() ]
new_RF_file = open(prefix + 'RF.txt', 'r')
new_RF = [ float(x) for x in new_RF_file.read().split() ]
reiterate = False
for index in range(0, len(old_RF)):
mean = 0.5 * (old_RF[index] + new_RF[index])
diff = math.fabs(0.5 * (old_RF[index] - new_RF[index]))
ratio = diff / mean
if ratio > convergence_change:
reiterate = True
if not reiterate:
printMessage('Exiting at iteration ' + str(iteration) + ' with ' + str(SF_voxel_count) + ' SF voxels due to unchanged response function coefficients')
shutil.copyfile(prefix + 'RF.txt', 'response.txt')
shutil.copyfile(prefix + 'SF.mif', 'voxels.mif')
break
# Go to the next iteration
# If we've terminated due to hitting the iteration limiter, we still need to copy the output file(s) to the correct location
if not os.path.exists('response.txt'):
printMessage('Exiting after maximum ' + str(lib.app.args.max_iters-1) + ' iterations with ' + str(SF_voxel_count) + ' SF voxels')
shutil.copyfile('iter' + str(lib.app.args.max_iters-1) + '_RF.txt', 'response.txt')
shutil.copyfile('iter' + str(lib.app.args.max_iters-1) + '_SF.mif', 'voxels.mif')
shutil.copyfile('response.txt', os.path.join(lib.app.workingDir, lib.app.args.output))
def execute():
import os, shutil
import lib.app
from lib.getImageStat import getImageStat
from lib.printMessage import printMessage
from lib.runCommand import runCommand
lmax_option = ''
if lib.app.args.lmax:
lmax_option = ' -lmax ' + lib.app.args.lmax
if lib.app.args.max_iters < 2:
errorMessage('Number of iterations must be at least 2')
runCommand('amp2sh dwi.mif dwiSH.mif' + lmax_option)
for iteration in range(0, lib.app.args.max_iters):
prefix = 'iter' + str(iteration) + '_'
if iteration == 0:
RF_in_path = 'init_RF.txt'
mask_in_path = 'mask.mif'
init_RF = '1 -1 1'
with open('init_RF.txt', 'w') as f:
f.write(init_RF)
iter_lmax_option = ' -lmax 4'
else:
RF_in_path = 'iter' + str(iteration - 1) + '_RF.txt'
mask_in_path = 'iter' + str(iteration - 1) + '_SF_dilated.mif'
iter_lmax_option = lmax_option
# Run CSD
runCommand('dwi2fod dwi.mif ' + RF_in_path + ' ' + prefix +
'FOD.mif -mask ' + mask_in_path + iter_lmax_option)
# Get amplitudes of two largest peaks, and direction of largest
# TODO Speed-test fod2fixel against sh2peaks
# TODO Add maximum number of fixels per voxel option to fod2fixel?
runCommand('fod2fixel ' + prefix + 'FOD.mif -peak ' + prefix +
'peaks.msf -mask ' + mask_in_path + ' -fmls_no_thresholds')
runCommand('fixel2voxel ' + prefix + 'peaks.msf split_value ' +
prefix + 'amps.mif')
runCommand('mrconvert ' + prefix + 'amps.mif ' + prefix +
'first_peaks.mif -coord 3 0 -axes 0,1,2')
runCommand('mrconvert ' + prefix + 'amps.mif ' + prefix +
'second_peaks.mif -coord 3 1 -axes 0,1,2')
runCommand('fixel2voxel ' + prefix + 'peaks.msf split_dir ' + prefix +
'all_dirs.mif')
runCommand('mrconvert ' + prefix + 'all_dirs.mif ' + prefix +
'first_dir.mif -coord 3 0:2')
# Calculate the 'cost function' Donald derived for selecting single-fibre voxels
# https://github.com/MRtrix3/mrtrix3/pull/426
# sqrt(|peak1|) * (1 - |peak2| / |peak1|)^2
runCommand('mrcalc ' + prefix + 'first_peaks.mif -sqrt 1 ' + prefix +
'second_peaks.mif ' + prefix +
'first_peaks.mif -div -sub 2 -pow -mult ' + prefix +
'CF.mif')
# Select the top-ranked voxels
runCommand('mrthreshold ' + prefix + 'CF.mif -top ' +
str(lib.app.args.sf_voxels) + ' ' + prefix + 'SF.mif')
# Generate a new response function based on this selection
runCommand('sh2response dwiSH.mif ' + prefix + 'SF.mif ' + prefix +
'first_dir.mif ' + prefix + 'RF.txt' + iter_lmax_option)
# Should we terminate?
if iteration > 0:
runCommand('mrcalc ' + prefix + 'SF.mif iter' +
str(iteration - 1) + '_SF.mif -sub ' + prefix +
'SF_diff.mif')
max_diff = getImageStat(prefix + 'SF_diff.mif', 'max')
if int(max_diff) == 0:
printMessage(
'Convergence of SF voxel selection detected at iteration '
+ str(iteration))
shutil.copyfile(prefix + 'RF.txt', 'response.txt')
shutil.copyfile(prefix + 'SF.mif', 'voxels.mif')
break
# Select a greater number of top single-fibre voxels, and dilate;
# these are the voxels that will be re-tested in the next iteration
runCommand('mrthreshold ' + prefix + 'CF.mif -top ' +
str(lib.app.args.iter_voxels) + ' - | maskfilter ' +
prefix + 'SF.mif dilate ' + prefix +
'SF_dilated.mif -npass ' + str(lib.app.args.dilate))
# Commence the next iteration
# If terminating due to running out of iterations, still need to put the results in the appropriate location
if not os.path.exists('response.txt'):
printMessage('Exiting after maximum ' +
str(lib.app.args.max_iters - 1) + ' iterations')
shutil.copyfile('iter' + str(lib.app.args.max_iters - 1) + '_RF.txt',
'response.txt')
shutil.copyfile('iter' + str(lib.app.args.max_iters - 1) + '_SF.mif',
'voxels.mif')
shutil.copyfile('response.txt',
os.path.join(lib.app.workingDir, lib.app.args.output))
def execute():
import math, os, shutil
import lib.app
from lib.getHeaderInfo import getHeaderInfo
from lib.getImageStat import getImageStat
from lib.getUserPath import getUserPath
from lib.printMessage import printMessage
from lib.runCommand import runCommand
from lib.warnMessage import warnMessage
from lib.errorMessage import errorMessage
# Get b-values and number of volumes per b-value.
bvalues = [
int(round(float(x)))
for x in getHeaderInfo('dwi.mif', 'shells').split()
]
bvolumes = [
int(x) for x in getHeaderInfo('dwi.mif', 'shellcounts').split()
]
printMessage(
str(len(bvalues)) + ' unique b-value(s) detected: ' +
','.join(map(str, bvalues)) + ' with ' + ','.join(map(str, bvolumes)) +
' volumes.')
if len(bvalues) < 2:
errorMessage('Need at least 2 unique b-values (including b=0).')
# Get lmax information (if provided).
sfwm_lmax = []
if lib.app.args.lmax:
sfwm_lmax = [int(x.strip()) for x in lib.app.args.lmax.split(',')]
if not len(sfwm_lmax) == len(bvalues):
errorMessage('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 l in sfwm_lmax:
if l % 2:
errorMessage(
'Values supplied to the -lmax option must be even.')
if l < 0:
errorMessage(
'Values supplied to the -lmax option must be non-negative.'
)
# Erode (brain) mask.
if lib.app.args.erode > 0:
runCommand('maskfilter mask.mif erode eroded_mask.mif -npass ' +
str(lib.app.args.erode))
else:
runCommand('mrconvert mask.mif eroded_mask.mif -datatype bit')
# Get volumes, compute mean signal and SDM per b-value; compute overall SDM; get rid of erroneous values.
totvolumes = 0
fullsdmcmd = 'mrcalc'
errcmd = 'mrcalc'
zeropath = 'mean_b' + str(bvalues[0]) + '.mif'
for i, b in enumerate(bvalues):
dwipath = 'dwi_b' + str(b) + '.mif'
runCommand('dwiextract dwi.mif -shell ' + str(b) + ' ' + dwipath)
meanpath = 'mean_b' + str(b) + '.mif'
runCommand('mrmath ' + dwipath + ' mean ' + meanpath + ' -axis 3')
errpath = 'err_b' + str(b) + '.mif'
runCommand('mrcalc ' + meanpath + ' -finite ' + meanpath +
' 0 -if 0 -le ' + errpath + ' -datatype bit')
errcmd += ' ' + errpath
if i > 0:
errcmd += ' -add'
sdmpath = 'sdm_b' + str(b) + '.mif'
runCommand('mrcalc ' + zeropath + ' ' + meanpath +
' -divide -log ' + sdmpath)
totvolumes += bvolumes[i]
fullsdmcmd += ' ' + sdmpath + ' ' + str(bvolumes[i]) + ' -mult'
if i > 1:
fullsdmcmd += ' -add'
fullsdmcmd += ' ' + str(totvolumes) + ' -divide full_sdm.mif'
runCommand(fullsdmcmd)
runCommand(
'mrcalc full_sdm.mif -finite full_sdm.mif 0 -if 0 -le err_sdm.mif -datatype bit'
)
errcmd += ' err_sdm.mif -add 0 eroded_mask.mif -if safe_mask.mif -datatype bit'
runCommand(errcmd)
runCommand('mrcalc safe_mask.mif full_sdm.mif 0 -if 10 -min safe_sdm.mif')
# Compute FA and principal eigenvectors; crude WM versus GM-CSF separation based on FA.
runCommand(
'dwi2tensor dwi.mif - -mask safe_mask.mif | tensor2metric - -fa safe_fa.mif -vector safe_vecs.mif -modulate none -mask safe_mask.mif'
)
runCommand('mrcalc safe_mask.mif safe_fa.mif 0 -if ' +
str(lib.app.args.fa) + ' -gt crude_wm.mif -datatype bit')
runCommand(
'mrcalc crude_wm.mif 0 safe_mask.mif -if _crudenonwm.mif -datatype bit'
)
# Crude GM versus CSF separation based on SDM.
crudenonwmmedian = getImageStat('safe_sdm.mif', 'median',
'_crudenonwm.mif')
runCommand(
'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'
)
runCommand(
'mrcalc crude_csf.mif 0 _crudenonwm.mif -if crude_gm.mif -datatype bit'
)
# Refine WM: remove high SDM outliers.
crudewmmedian = getImageStat('safe_sdm.mif', 'median', 'crude_wm.mif')
runCommand('mrcalc crude_wm.mif safe_sdm.mif 0 -if ' + str(crudewmmedian) +
' -gt _crudewmhigh.mif -datatype bit')
runCommand(
'mrcalc _crudewmhigh.mif 0 crude_wm.mif -if _crudewmlow.mif -datatype bit'
)
crudewmQ1 = float(getImageStat('safe_sdm.mif', 'median',
'_crudewmlow.mif'))
crudewmQ3 = float(
getImageStat('safe_sdm.mif', 'median', '_crudewmhigh.mif'))
crudewmoutlthresh = crudewmQ3 + (crudewmQ3 - crudewmQ1)
runCommand('mrcalc crude_wm.mif safe_sdm.mif 0 -if ' +
str(crudewmoutlthresh) +
' -gt _crudewmoutliers.mif -datatype bit')
runCommand(
'mrcalc _crudewmoutliers.mif 0 crude_wm.mif -if refined_wm.mif -datatype bit'
)
# Refine GM: separate safer GM from partial volumed voxels.
crudegmmedian = getImageStat('safe_sdm.mif', 'median', 'crude_gm.mif')
runCommand('mrcalc crude_gm.mif safe_sdm.mif 0 -if ' + str(crudegmmedian) +
' -gt _crudegmhigh.mif -datatype bit')
runCommand(
'mrcalc _crudegmhigh.mif 0 crude_gm.mif -if _crudegmlow.mif -datatype bit'
)
runCommand(
'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'
)
runCommand(
'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'
)
runCommand(
'mrcalc _crudegmhighselect.mif 1 _crudegmlowselect.mif -if refined_gm.mif -datatype bit'
)
# Refine CSF: recover lost CSF from crude WM SDM outliers, separate safer CSF from partial volumed voxels.
crudecsfmin = getImageStat('safe_sdm.mif', 'min', 'crude_csf.mif')
runCommand('mrcalc _crudewmoutliers.mif safe_sdm.mif 0 -if ' +
str(crudecsfmin) +
' -gt 1 crude_csf.mif -if _crudecsfextra.mif -datatype bit')
runCommand(
'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'
)
# Get final voxels for single-fibre WM response function estimation from WM using 'tournier' algorithm.
refwmcount = float(
getImageStat('refined_wm.mif', 'count', 'refined_wm.mif'))
voxsfwmcount = int(round(refwmcount * lib.app.args.sfwm / 100.0))
printMessage('Running \'tournier\' algorithm to select ' +
str(voxsfwmcount) + ' single-fibre WM voxels.')
cleanopt = ''
if not lib.app.cleanup:
cleanopt = ' -nocleanup'
runCommand(
'dwi2response tournier dwi.mif _respsfwmss.txt -sf_voxels ' +
str(voxsfwmcount) + ' -iter_voxels ' + str(voxsfwmcount * 10) +
' -mask refined_wm.mif -voxels voxels_sfwm.mif -quiet -tempdir ' +
lib.app.tempDir + cleanopt)
# Get final voxels for GM response function estimation from GM.
refgmmedian = getImageStat('safe_sdm.mif', 'median', 'refined_gm.mif')
runCommand('mrcalc refined_gm.mif safe_sdm.mif 0 -if ' + str(refgmmedian) +
' -gt _refinedgmhigh.mif -datatype bit')
runCommand(
'mrcalc _refinedgmhigh.mif 0 refined_gm.mif -if _refinedgmlow.mif -datatype bit'
)
refgmhighcount = float(
getImageStat('_refinedgmhigh.mif', 'count', '_refinedgmhigh.mif'))
refgmlowcount = float(
getImageStat('_refinedgmlow.mif', 'count', '_refinedgmlow.mif'))
voxgmhighcount = int(round(refgmhighcount * lib.app.args.gm / 100.0))
voxgmlowcount = int(round(refgmlowcount * lib.app.args.gm / 100.0))
runCommand(
'mrcalc _refinedgmhigh.mif safe_sdm.mif 0 -if - | mrthreshold - - -bottom '
+ str(voxgmhighcount) +
' -ignorezero | mrcalc _refinedgmhigh.mif - 0 -if _refinedgmhighselect.mif -datatype bit'
)
runCommand(
'mrcalc _refinedgmlow.mif safe_sdm.mif 0 -if - | mrthreshold - - -top '
+ str(voxgmlowcount) +
' -ignorezero | mrcalc _refinedgmlow.mif - 0 -if _refinedgmlowselect.mif -datatype bit'
)
runCommand(
'mrcalc _refinedgmhighselect.mif 1 _refinedgmlowselect.mif -if voxels_gm.mif -datatype bit'
)
# Get final voxels for CSF response function estimation from CSF.
refcsfcount = float(
getImageStat('refined_csf.mif', 'count', 'refined_csf.mif'))
voxcsfcount = int(round(refcsfcount * lib.app.args.csf / 100.0))
runCommand(
'mrcalc refined_csf.mif safe_sdm.mif 0 -if - | mrthreshold - - -top ' +
str(voxcsfcount) +
' -ignorezero | mrcalc refined_csf.mif - 0 -if voxels_csf.mif -datatype bit'
)
# Show summary of voxels counts.
textarrow = ' --> '
printMessage('Summary of voxel counts:')
printMessage(
'Mask: ' + str(int(getImageStat('mask.mif', 'count', 'mask.mif'))) +
textarrow +
str(int(getImageStat('eroded_mask.mif', 'count', 'eroded_mask.mif'))) +
textarrow +
str(int(getImageStat('safe_mask.mif', 'count', 'safe_mask.mif'))))
printMessage(
'WM: ' +
str(int(getImageStat('crude_wm.mif', 'count', 'crude_wm.mif'))) +
textarrow +
str(int(getImageStat('refined_wm.mif', 'count', 'refined_wm.mif'))) +
textarrow +
str(int(getImageStat('voxels_sfwm.mif', 'count', 'voxels_sfwm.mif'))) +
' (SF)')
printMessage(
'GM: ' +
str(int(getImageStat('crude_gm.mif', 'count', 'crude_gm.mif'))) +
textarrow +
str(int(getImageStat('refined_gm.mif', 'count', 'refined_gm.mif'))) +
textarrow +
str(int(getImageStat('voxels_gm.mif', 'count', 'voxels_gm.mif'))))
printMessage(
'CSF: ' +
str(int(getImageStat('crude_csf.mif', 'count', 'crude_csf.mif'))) +
textarrow +
str(int(getImageStat('refined_csf.mif', 'count', 'refined_csf.mif'))) +
textarrow +
str(int(getImageStat('voxels_csf.mif', 'count', 'voxels_csf.mif'))))
# Generate single-fibre WM, GM and CSF responses
sfwm_responses = []
gm_responses = []
csf_responses = []
max_length = 0
for index, b in enumerate(bvalues):
dwipath = 'dwi_b' + str(b) + '.mif'
this_b_lmax_option = ''
if sfwm_lmax:
this_b_lmax_option = ' -lmax ' + str(sfwm_lmax[index])
runCommand(
'amp2sh ' + dwipath +
' - | sh2response - voxels_sfwm.mif safe_vecs.mif _respsfwmb' +
str(b) + '.txt' + this_b_lmax_option)
sfwm_response = open('_respsfwmb' + str(b) + '.txt',
'r').read().split()
sfwm_responses.append(sfwm_response)
max_length = max(max_length, len(sfwm_response))
meanpath = 'mean_b' + str(b) + '.mif'
gm_mean = float(getImageStat(meanpath, 'mean', 'voxels_gm.mif'))
csf_mean = float(getImageStat(meanpath, 'mean', 'voxels_csf.mif'))
gm_responses.append(str(gm_mean * math.sqrt(4.0 * math.pi)))
csf_responses.append(str(csf_mean * math.sqrt(4.0 * math.pi)))
with open('response_sfwm.txt', 'w') as f:
for line in sfwm_responses:
line += ['0'] * (max_length - len(line))
f.write(' '.join(line) + '\n')
with open('response_gm.txt', 'w') as f:
for line in gm_responses:
f.write(line + '\n')
with open('response_csf.txt', 'w') as f:
for line in csf_responses:
f.write(line + '\n')
shutil.copyfile('response_sfwm.txt',
getUserPath(lib.app.args.out_sfwm, False))
shutil.copyfile('response_gm.txt', getUserPath(lib.app.args.out_gm, False))
shutil.copyfile('response_csf.txt', getUserPath(lib.app.args.out_csf,
False))
# Generate 4D binary images with voxel selection at major stages in algorithm (RGB as in MSMT-CSD paper).
runCommand(
'mrcat crude_csf.mif crude_gm.mif crude_wm.mif crude.mif -axis 3')
runCommand(
'mrcat refined_csf.mif refined_gm.mif refined_wm.mif refined.mif -axis 3'
)
runCommand(
'mrcat voxels_csf.mif voxels_gm.mif voxels_sfwm.mif voxels.mif -axis 3'
)
