def implement(self):
dwi = self.getBackupImage('dwi')
bEncs = self.getBackupImage('grad', None, 'b')
bVals = self.getBackupImage('grad', None, 'bvals')
bVecs = self.getBackupImage('grad', None, 'bvecs')
(bEncs, bVecs,
bVals) = self.__produceEncodingFiles(bEncs, bVecs, bVals,
dwi) # Convert bvecs bval
expectedLayout = self.get('stride_orientation')
if not mriutil.isDataStridesOrientationExpected(dwi, expectedLayout) \
and self.get("force_realign_strides"):
self.warning("Reorienting strides for image {}".format(dwi))
self.__stride4DImage(dwi, bEncs, bVecs, bVals, expectedLayout)
else:
self.info("Linking {} to {}".format(
dwi, util.symlink(dwi, self.workingDir)))
images = Images(
(self.getBackupImage('anat'), 'high resolution'),
(self.getBackupImage('b0_pa'), 'B0 posterior to anterior'),
(self.getBackupImage('b0_ap'), 'B0 anterior to posterior'),
(self.getBackupImage('mag'), 'MR magnitude'),
(self.getBackupImage('phase'), 'MR phase '),
(self.getBackupImage('aparc_aseg'), 'parcellation'),
(self.getBackupImage('anat',
'freesurfer'), 'freesurfer anatomical'),
(self.getBackupImage('lh_ribbon'), 'left hemisphere ribbon'),
(self.getBackupImage('rh_ribbon'), 'right hemisphere ribbon'),
(self.getBackupImage('brodmann'), 'brodmann'),
)
for image, description in images.getData():
if image:
if not mriutil.isDataStridesOrientationExpected(image, expectedLayout) \
and self.get("force_realign_strides"):
self.info(
mriutil.stride3DImage(image,
self.buildName(image, "stride"),
expectedLayout))
else:
self.info("Found {} image, linking {} to {}".format(
description, image,
util.symlink(image, self.workingDir)))
for directory in [
os.path.join(self.backupDir, directory)
for directory in os.listdir(self.backupDir)
if os.path.isdir(os.path.join(self.backupDir, directory))
]:
if mriutil.isAfreesurferStructure(directory):
self.info(
"{} seem\'s a valid freesurfer structure: linking to {} directory"
.format(directory, self.workingDir))
util.symlink(directory, self.workingDir,
self.get("parcellation", "id"))
def implement(self):
self.info("Build directories structure for subject: {}".format(os.path.basename(self.workingDir)))
#@TODO add description to that struct
images = Images((self.getSubjectImage('anat'), ""),
(self.getSubjectImage('dwi'), ""),
(self.getSubjectImage('mag',), ""),
(self.getSubjectImage('phase'), ""),
(self.getSubjectImage('aparc_aseg'), ""),
(self.getSubjectImage('anat', 'freesurfer'), ""),
(self.getSubjectImage('lh_ribbon'), ""),
(self.getSubjectImage('rh_ribbon'), ""),
(self.getSubjectImage('brodmann'), ""),
(self.getSubjectImage('b0_ap'), ""),
(self.getSubjectImage('b0_pa'), ""),
(self.getSubjectImage('grad', None, 'b'), ""),
(self.getSubjectImage('grad', None, 'bvals'), ""),
(self.getSubjectImage('grad', None, 'bvecs'), ""),
(self.getSubjectImage('tq_dict', None, 'qry'), ""),
(self.getSubjectImage('queries', None, 'qry'), ""),
(self.getSubjectImage('config', None, 'cfg'), ""),)
for image, description in images.getData():
if image:
self.info("Found {} image: moving it to {} directory".format(description, image, self.workingDir))
shutil.move(image, self.workingDir)
directories = [os.path.join(self.subjectDir, directory) for directory in os.listdir(self.subjectDir) if os.path.isdir(os.path.join(self.subjectDir, directory))]
for directory in directories:
if mriutil.isAfreesurferStructure(directory):
self.info("{} seem\'s a valid freesurfer structure: moving it to {} directory".format(directory, self.workingDir))
shutil.move(directory, self.workingDir)
def implement(self):
self.info("Build directories structure for subject: {}".format(
os.path.basename(self.workingDir)))
#@TODO add description to that struct
images = Images((self.getSubjectImage('anat'), ""),
(self.getSubjectImage('dwi'), ""),
(self.getSubjectImage('mag',), ""),
(self.getSubjectImage('phase'), ""),
(self.getSubjectImage('aparc_aseg'), ""),
(self.getSubjectImage('anat', 'freesurfer'), ""),
(self.getSubjectImage('lh_ribbon'), ""),
(self.getSubjectImage('rh_ribbon'), ""),
(self.getSubjectImage('brodmann'), ""),
(self.getSubjectImage('b0_ap'), ""),
(self.getSubjectImage('b0_pa'), ""),
(self.getSubjectImage('grad', None, 'b'), ""),
(self.getSubjectImage('grad', None, 'bvals'), ""),
(self.getSubjectImage('grad', None, 'bvecs'), ""),
(self.getSubjectImage('tq_dict', None, 'qry'), ""),
(self.getSubjectImage('queries', None, 'qry'), ""),
(self.getSubjectImage('config', None, 'cfg'), ""),)
for image, description in images.getData():
if image:
self.info("Found {} image: moving it to {} directory".format(
description, image, self.workingDir))
shutil.move(image, self.workingDir)
directories = []
for directory in os.listdir(self.subjectDir):
target = os.path.join(self.subjectDir, directory)
if os.path.isdir(target):
directories.append(target)
for directory in directories:
if mriutil.isAfreesurferStructure(directory):
self.info("{} seem\'s a valid freesurfer structure: moving it to {} directory".format(directory, self.workingDir))
if os.path.islink(directory):
os.chdir(self.subjectDir)
# We need to chdir because `directory` is in
# `self.subjectDir` and we need `os.path.abspath` to
# work correctly
fsDirName = os.path.basename(directory)
linkto = os.path.abspath(os.readlink(directory))
newLinkto = os.path.relpath(linkto, self.workingDir)
newTarget = os.path.join(self.workingDir, fsDirName)
os.symlink(newLinkto, newTarget)
os.unlink(directory)
os.chdir(self.workingDir)
else:
shutil.move(directory, self.workingDir)
def __findAndLinkFreesurferStructure(self):
"""Look if a freesurfer structure already exists in the backup.
freesurfer structure will be link and id will be update
Returns:
Return the linked directory name if a freesurfer structure is found, False otherwise
"""
freesurferStructure = os.path.join(self.preparationDir, self.id)
if mriutil.isAfreesurferStructure(freesurferStructure):
self.info("{} seem\'s a valid freesurfer structure: moving it to {} directory".format(freesurferStructure, self.workingDir))
util.symlink(freesurferStructure, self.id)
return True
return False
def __findAndLinkFreesurferStructure(self):
"""Look if a freesurfer structure already exists in the backup.
freesurfer structure will be link and id will be update
Returns:
Return the linked directory name if a freesurfer structure is found, False otherwise
"""
freesurferStructure = os.path.join(self.preparationDir, self.id)
if mriutil.isAfreesurferStructure(freesurferStructure):
self.info(
"{} seem\'s a valid freesurfer structure: moving it to {} directory"
.format(freesurferStructure, self.workingDir))
util.symlink(freesurferStructure, self.workingDir, self.id)
return True
return False
def implement(self):
dwi = self.getBackupImage('dwi')
bEncs = self.getBackupImage('grad', None, 'b')
bVals = self.getBackupImage('grad', None, 'bvals')
bVecs = self.getBackupImage('grad', None, 'bvecs')
(bEncs, bVecs, bVals) = self.__produceEncodingFiles(bEncs, bVecs, bVals, dwi) # Convert bvecs bval
expectedLayout = self.get('stride_orientation')
if not mriutil.isDataStridesOrientationExpected(dwi, expectedLayout) \
and self.get("force_realign_strides"):
self.warning("Reorienting strides for image {}".format(dwi))
self.__stride4DImage(dwi, bEncs, bVecs, bVals, expectedLayout)
else:
self.info("Linking {} to {}".format(dwi, util.symlink(dwi, self.workingDir)))
images = Images(
(self.getBackupImage('anat'),'high resolution'),
(self.getBackupImage('b0_pa'),'B0 posterior to anterior'),
(self.getBackupImage('b0_ap'),'B0 anterior to posterior'),
(self.getBackupImage('mag'),'MR magnitude'),
(self.getBackupImage('phase'),'MR phase '),
(self.getBackupImage('aparc_aseg'),'parcellation'),
(self.getBackupImage('anat', 'freesurfer'),'freesurfer anatomical'),
(self.getBackupImage('lh_ribbon'),'left hemisphere ribbon'),
(self.getBackupImage('rh_ribbon'),'right hemisphere ribbon'),
(self.getBackupImage('brodmann'),'brodmann'),
)
for image, description in images.getData():
if image:
if not mriutil.isDataStridesOrientationExpected(image, expectedLayout) \
and self.get("force_realign_strides"):
self.info(mriutil.stride3DImage(image, self.buildName(image, "stride"), expectedLayout))
else:
self.info("Found {} image, linking {} to {}".format(description, image, util.symlink(image, self.workingDir)))
for directory in [os.path.join(self.backupDir, directory) for directory in os.listdir(self.backupDir) if os.path.isdir(os.path.join(self.backupDir, directory))]:
if mriutil.isAfreesurferStructure(directory):
self.info("{} seem\'s a valid freesurfer structure: linking to {} directory".format(directory, self.workingDir))
util.symlink(directory, self.workingDir, self.get("parcellation", "id"))
def implement(self):
self.info("Build directories structure for subject: {}".format(os.path.basename(self.workingDir)))
# @TODO add description to that struct
images = Images(
(self.getSubjectImage("anat"), ""),
(self.getSubjectImage("dwi"), ""),
(self.getSubjectImage("mag"), ""),
(self.getSubjectImage("phase"), ""),
(self.getSubjectImage("aparc_aseg"), ""),
(self.getSubjectImage("anat", "freesurfer"), ""),
(self.getSubjectImage("lh_ribbon"), ""),
(self.getSubjectImage("rh_ribbon"), ""),
(self.getSubjectImage("brodmann"), ""),
(self.getSubjectImage("b0_ap"), ""),
(self.getSubjectImage("b0_pa"), ""),
(self.getSubjectImage("grad", None, "b"), ""),
(self.getSubjectImage("grad", None, "bvals"), ""),
(self.getSubjectImage("grad", None, "bvecs"), ""),
(self.getSubjectImage("config", None, "cfg"), ""),
)
for image, description in images.getData():
if image:
self.info("Found {} image: moving it to {} directory".format(description, image, self.workingDir))
shutil.move(image, self.workingDir)
directories = [
os.path.join(self.subjectDir, directory)
for directory in os.listdir(self.subjectDir)
if os.path.isdir(os.path.join(self.subjectDir, directory))
]
for directory in directories:
if mriutil.isAfreesurferStructure(directory):
self.info(
"{} seem's a valid freesurfer structure: moving it to {} directory".format(
directory, self.workingDir
)
)
shutil.move(directory, self.workingDir)
def meetRequirement(self):
freesurferStructure = os.path.join(self.preparationDir, self.id)
if not mriutil.isAfreesurferStructure(freesurferStructure):
return False
else:
return Images((self.getPreparationImage('anat'), 'high resolution'))
def __isAValidStructure(self):
"""Determine if the directory is a valid structure
Returns:
a Boolean that represent if the subject integrity test pass for that directory
"""
#Anatomical, Dwi and gradient encoding direction are mandatory input
anat = util.getImage(self.config, self.workingDir, 'anat')
if not anat:
if util.getImage(self.config, self.workingDir, 'anat', None, 'nii'):
self.warning("Found some uncompressed nifti images into {} directory. "
"Please gzip those images and resubmit the pipeline again".format(self.workingDir))
return False
self.warning("No high resolution image found into {} directory".format(self.workingDir))
return False
dwi = util.getImage(self.config, self.workingDir, 'dwi')
if not dwi:
if util.getImage(self.config, self.workingDir, 'dwi', None, 'nii'):
self.warning("Found some uncompressed nifti image into {} directory. "
"Please gzip those images and resubmit the pipeline again".format(self.workingDir))
return False
self.warning("No diffusion weight image found into {} directory".format(self.workingDir))
return False
bEnc = util.getImage(self.config, self.workingDir,'grad', None, 'b')
bVals = util.getImage(self.config, self.workingDir,'grad', None, 'bvals')
bVecs = util.getImage(self.config, self.workingDir,'grad', None, 'bvecs')
directories = []
for directory in os.listdir(self.workingDir):
target = os.path.join(self.workingDir, directory)
if os.path.isdir(target):
directories.append(target)
validFS = False
for directory in directories:
if mriutil.isAfreesurferStructure(directory):
validFS = True
if not validFS:
self.warning("No valid freesurfer directory found in: {}".format(self.workingDir))
return False
if (not bEnc) and (not bVals or not bVecs):
self.warning("No valid .b encoding or (.bvals, .bvecs) files found in directory: {}".format(self.workingDir))
return False
else:
nbDirections = mriutil.getNbDirectionsFromDWI(dwi)
if nbDirections <= 45:
msg = "Found only {} directions into {} image. Hardi model will not be accurate with diffusion weighted image " \
"that contain less than 45 directions\n\n".format(nbDirections, dwi)
self.warning(msg)
#return False
if bEnc and not self.__isValidEncoding(nbDirections, '.b'):
self.warning("Encoding file {} is invalid".format(bEnc))
return False
if bVals and not self.__isValidEncoding(nbDirections, '.bvals'):
self.warning("Encoding file {} is invalid".format(bEnc))
return False
if bVecs and not self.__isValidEncoding(nbDirections, '.bvecs'):
self.warning("Encoding file {} is invalid".format(bVecs))
return False
#Validate optionnal images
images = {
'anat': (anat, 'high resolution'),
'dwi': (dwi,'diffusion weighted'),
'mag': (util.getImage(self.config, self.workingDir, 'mag'), 'MR magnitude '),
'phase': (util.getImage(self.config, self.workingDir, 'phase'), 'MR phase '),
'b0_ap': (util.getImage(self.config, self.workingDir, 'b0_ap'), "posterior to anterior b0 "),
'b0_pa': (util.getImage(self.config, self.workingDir, 'b0_pa'), "anterior to posterior b0")}
if self.config.get('arguments', 'debug') == 'True':
self.debug("Images found into {} directory: {}".format(self.workingDir, images))
if self.config.getboolean('arguments', 'prompt'):
for key, (value, description) in images.iteritems():
if value:
if not mriutil.isDataStridesOrientationExpected(value, self.config.get('preparation', 'stride_orientation'))\
and self.config.getboolean("preparation", "force_realign_strides"):
msg = "Data strides layout for {} is unexpected and force_realign_strides is set to True.\n \
If you continue, all unexpected images will be realign accordingly.\n\
Only a copy of the original images will be alter.".format(value)
if not util.displayYesNoMessage(msg):
self.warning("Remove this subject from the list?")
return False
else:
break
#if one and only one b0 image is given, make sure that the b0 image is not on same direction than the dwi.
if (not (images['b0_ap'][0] and images['b0_pa'][0])) and (images['b0_ap'][0] or images['b0_pa'][0]) \
and (self.config.get("correction", "ignore") == "False"):
if ((self.config.get("correction", "phase_enc_dir") == "0") and images['b0_pa'][0]) \
or ((self.config.get("correction", "phase_enc_dir") == "1") and images['b0_ap'][0]):
msg = "Found only one B0 image into the subject directory and that B0 is in " \
"the same phase encoding direction than the DWI.\n" \
"We recommend to remove the B0 image so at least a motion correction will be perform"
if not util.displayYesNoMessage(msg):
self.warning("Remove this subject from the list?")
return False
if images['mag'][0] and images['phase'][0] and (images['b0_ap'][0] or images['b0_pa'][0]):
msg = "Found both Fieldmap and B0 images into the subject directory\n" \
"We recommend to disabled fieldmap correction?"
if not util.displayYesNoMessage(msg):
self.warning("Remove this subject from the list?")
return False
return True