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fsscript.py
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#!/usr/bin/env python
import argparse
import os
import shutil
import SimpleITK as sitk
import subprocess
from PipeLineFunctionHelpers import mkdir_p, make_dummy_file
def normalizeWM(t1, wm_prob):
"""This function will compute the mean value of wm and rescale the image so that the mean WM=100"""
WM_MEAN_FINAL = 110.0
WM_THRESHOLD = 0.66
wm_mask = sitk.BinaryThreshold(wm_prob, WM_THRESHOLD)
ls = sitk.LabelStatisticsImageFilter()
ls.Execute(t1, wm_mask)
wm_value = 1
myMeasurementMap = ls.GetMeasurementMap(wm_value)
MeanWM = myMeasurementMap['Mean']
t1_new = sitk.Cast(sitk.Cast(t1, sitk.sitkFloat32) * WM_MEAN_FINAL / MeanWM, sitk.sitkUInt8)
return t1_new
def IsFirstNewerThanSecond(firstFile, secondFile):
if not os.path.exists(firstFile):
print "ERROR: image missing", firstFile
return True
if not os.path.exists(secondFile):
print "Returning True because file is missing: {0}".format(secondFile)
return True
image_time = os.path.getmtime(firstFile)
reference_time = os.path.getmtime(secondFile)
if image_time > reference_time:
print "Returning True because {0} is newer than {1}".format(firstFile, secondFile)
return True
return False
def run_mri_convert_script(niftiVol, mgzVol, subjects_dir, subj_session_id, FREESURFER_HOME, FS_SCRIPT):
FS_SCRIPT_FN = os.path.join(FREESURFER_HOME, FS_SCRIPT)
mri_convert_script = """#!/bin/bash
#$ -o {FSSUBJDIR}/{SUBJ_SESSION_ID}/scripts/mri_convert_qsub.out
#$ -e {FSSUBJDIR}/{SUBJ_SESSION_ID}/scripts/mri_convert_qsub.err
#$ -cwd
export FREESURFER_HOME={FSHOME}
export SUBJECTS_DIR={FSSUBJDIR}
source {SOURCE_SCRIPT}
{FSHOME}/bin/mri_convert --conform --out_data_type uchar {invol} {outvol}
status=$?
exit $status
""".format(SOURCE_SCRIPT=FS_SCRIPT_FN,
FSHOME=FREESURFER_HOME,
FSSUBJDIR=subjects_dir,
SUBJ_SESSION_ID=subj_session_id,
invol=niftiVol,
outvol=mgzVol)
script_name = mgzVol + '_convert.sh'
script = open(script_name, 'w')
script.write(mri_convert_script)
script.close()
os.chmod(script_name, 0777)
script_name_stdout = mgzVol + '_convert.out'
script_name_stdout_fid = open(script_name_stdout, 'w')
print "Starting mri_convert"
scriptStatus = subprocess.check_call([script_name], stdout=script_name_stdout_fid, stderr=subprocess.STDOUT, shell='/bin/bash')
if scriptStatus != 0:
sys.exit(scriptStatus)
print "Ending mri_convert"
script_name_stdout_fid.close()
return
def run_mri_mask_script(output_brainmask_fn_mgz, output_custom_brainmask_fn_mgz, output_nu_fn_mgz, subjects_dir, subj_session_id, FREESURFER_HOME, FS_SCRIPT):
FS_SCRIPT_FN = os.path.join(FREESURFER_HOME, FS_SCRIPT)
mri_mask_script = """#!/bin/bash
#$ -o {FSSUBJDIR}/{SUBJ_SESSION_ID}/scripts/mri_mask_scipt_qsub.out
#$ -e {FSSUBJDIR}/{SUBJ_SESSION_ID}/scripts/mri_mask_scipt_qsub.err
#$ -cwd
export FREESURFER_HOME={FSHOME}
export SUBJECTS_DIR={FSSUBJDIR}
source {SOURCE_SCRIPT}
{FSHOME}/bin/mri_add_xform_to_header -c {CURRENT}/transforms/talairach.xfm {maskvol} {maskvol}
{FSHOME}/bin/mri_mask {invol} {maskvol} {outvol}
status=$?
exit $status
""".format(SOURCE_SCRIPT=FS_SCRIPT_FN,
FSHOME=FREESURFER_HOME,
FSSUBJDIR=subjects_dir,
SUBJ_SESSION_ID=subj_session_id,
CURRENT=os.path.dirname(output_custom_brainmask_fn_mgz),
invol=output_nu_fn_mgz,
maskvol=output_custom_brainmask_fn_mgz,
# regmaskvol=output_custom_brainmask_fn_mgz.replace(".mgz", "_reg.mgz"),
outvol=output_brainmask_fn_mgz)
script_name = output_brainmask_fn_mgz + '_mask.sh'
script = open(script_name, 'w')
script.write(mri_mask_script)
script.close()
os.chmod(script_name, 0777)
script_name_stdout = output_brainmask_fn_mgz + '_convert.out'
script_name_stdout_fid = open(script_name_stdout, 'w')
print "Starting mri_mask"
scriptStatus = subprocess.check_call([script_name], stdout=script_name_stdout_fid, stderr=subprocess.STDOUT, shell='/bin/bash')
if scriptStatus != 0:
sys.exit(scriptStatus)
print "Ending mri_mask"
script_name_stdout_fid.close()
return
def baw_FixBrainMask(brainmask, subjects_dir, FREESURFER_HOME, FS_SCRIPT, subj_session_id):
base_subj_dir = os.path.join(subjects_dir, subj_session_id, 'mri')
mkdir_p(base_subj_dir)
output_brainmask_fn_mgz = os.path.join(base_subj_dir, 'brainmask.mgz')
output_custom_brainmask_fn = os.path.join(base_subj_dir, 'custom_brain_mask.nii.gz')
output_custom_brainmask_fn_mgz = os.path.join(base_subj_dir, 'custom_brain_mask.mgz')
output_nu_fn_mgz = os.path.join(base_subj_dir, 'nu.mgz')
if IsFirstNewerThanSecond(brainmask, output_brainmask_fn_mgz) \
or IsFirstNewerThanSecond(brainmask, output_nu_fn_mgz) \
or IsFirstNewerThanSecond(output_nu_fn_mgz, output_custom_brainmask_fn_mgz):
print "Fixing BrainMask recon-auto1 stage"
brain = sitk.ReadImage(brainmask)
blood = sitk.BinaryThreshold(brain, 5, 5)
not_blood = 1 - blood
clipping = sitk.BinaryThreshold(brain, 1, 1000000) - blood
fill_size = 2
## HACK: Unfortunately we need to hole fill because of a WM bug in BABC where
## some white matter is being classified as background when it it being avoid due
## to too strict of multi-modal thresholding.
hole_filled = sitk.ErodeObjectMorphology(sitk.DilateObjectMorphology(clipping, fill_size), fill_size)
final_mask = sitk.Cast(hole_filled * not_blood, sitk.sitkUInt8)
## Now make an mgz version of the binary custom brain mask
sitk.WriteImage(final_mask, output_custom_brainmask_fn) ## brain_matter mask with blood zero'ed out, and no "NOT" regions.
run_mri_convert_script(output_custom_brainmask_fn, output_custom_brainmask_fn_mgz, subjects_dir,subj_session_id, FREESURFER_HOME, FS_SCRIPT)
os.rename(output_brainmask_fn_mgz, output_brainmask_fn_mgz.replace('.mgz','_orig_backup.mgz'))
## Multipy output_brainmask_fn_mgz = output_custom_brainmask_fn_mgz * output_nu_fn_mgz
run_mri_mask_script(output_brainmask_fn_mgz, output_custom_brainmask_fn_mgz, output_nu_fn_mgz, subjects_dir, subj_session_id, FREESURFER_HOME, FS_SCRIPT)
else:
print "NOTHING TO BE DONE, SO SKIPPING."
return # Nothing to be done, files are already up-to-date.
def removeDir(path):
if os.path.isdir(path):
shutil.rmtree(path)
def runAutoReconStage(subj_session_id, StageToRun, t1_fn, subjects_dir, FREESURFER_HOME, FS_SCRIPT):
FS_SCRIPT_FN = os.path.join(FREESURFER_HOME, FS_SCRIPT)
base_subj_dir = os.path.join(subjects_dir, subj_session_id)
orig_001_mgz_fn = os.path.join(base_subj_dir,'mri','orig','001.mgz')
if IsFirstNewerThanSecond(t1_fn, orig_001_mgz_fn):
if os.path.exists(base_subj_dir):
removeDir(base_subj_dir)
mkdir_p(os.path.dirname(orig_001_mgz_fn))
run_mri_convert_script(t1_fn, orig_001_mgz_fn, subjects_dir, subj_session_id, FREESURFER_HOME, FS_SCRIPT)
auto_recon_script="""#!/bin/bash
#$ -o {FSSUBJDIR}/{SUBJ_SESSION_ID}/scripts/autorecon{AUTORECONSTAGE}_qsub.out
#$ -e {FSSUBJDIR}/{SUBJ_SESSION_ID}/scripts/autorecon{AUTORECONSTAGE}_qsub.err
#$ -cwd
export FREESURFER_HOME={FSHOME}
export SUBJECTS_DIR={FSSUBJDIR}
source {SOURCE_SCRIPT}
## Need to delete the "IsRunning" flags, if nipype pipeline is running this, then nipype prevents duplicates
rm -f {FSSUBJDIR}/{SUBJ_SESSION_ID}/scripts/Is*
{FSHOME}/bin/recon-all -debug -subjid {SUBJ_SESSION_ID} -make autorecon{AUTORECONSTAGE}
status=$?
exit $status
""".format(SOURCE_SCRIPT=FS_SCRIPT_FN,
FSHOME=FREESURFER_HOME,
FSSUBJDIR=subjects_dir,
AUTORECONSTAGE=StageToRun,
SUBJ_SESSION_ID=subj_session_id)
base_run_dir = os.path.join(subjects_dir, subj_session_id, 'scripts')
mkdir_p(base_run_dir)
script_name = os.path.join(base_run_dir,'run_autorecon_stage'+str(StageToRun)+'.sh')
script = open(script_name, 'w')
script.write(auto_recon_script)
script.close()
os.chmod(script_name, 0777)
script_name_stdout = script_name + '_out'
script_name_stdout_fid = open(script_name_stdout, 'w')
print "Starting auto_recon Stage: {0} for SubjectSession {1}".format(StageToRun, subj_session_id)
scriptStatus = subprocess.check_call([script_name], stdout=script_name_stdout_fid, stderr=subprocess.STDOUT, shell='/bin/bash')
if scriptStatus != 0:
sys.exit(scriptStatus)
print "Ending auto_recon Stage: {0} for SubjectSession {1}".format(StageToRun, subj_session_id)
script_name_stdout_fid.close()
return
def runSubjectTemplate(args, FREESURFER_HOME, FS_SCRIPT):
""" Create the within-subject template """
base_template_id = args.base_template_id
list_all_subj_session_ids = args.list_all_subj_session_ids
subjects_dir = args.subjects_dir
print "X"*80
print "base_template_id :{0}:".format(base_template_id)
print "Input a list of list_all_subj_session_ids :{0}:".format(list_all_subj_session_ids)
print "subjects_dir :{0}:".format(subjects_dir)
print "X"*80
assert isinstance(list_all_subj_session_ids, list), "Must input a list of list_all_subj_session_ids :{0}:".format(list_all_subj_session_ids)
StageToRun = "Within-SubjectTemplate"
FS_SCRIPT_FN = os.path.join(FREESURFER_HOME, FS_SCRIPT)
allTimePointFlags = ""
for subj_session_id in list_all_subj_session_ids:
allTimePointFlags += " -tp {timepoint}".format(timepoint=subj_session_id)
allTimePointFlags += " -all"
auto_recon_script="""#!/bin/bash
#$ -o {FSSUBJDIR}/{TEMPLATEID}/scripts/base_{TEMPLATEID}_qsub.out
#$ -e {FSSUBJDIR}/{TEMPLATEID}/scripts/base_{TEMPLATEID}_qsub.err
#$ -cwd
export FREESURFER_HOME={FSHOME}
export SUBJECTS_DIR={FSSUBJDIR}
source {SOURCE_SCRIPT}
## Need to delete the "IsRunning" flags, if nipype pipeline is running this, then nipype prevents duplicates
rm -f {FSSUBJDIR}/{TEMPLATEID}/scripts/Is*
if [ -f {FSSUBJDIR}/{TEMPLATEID}/stats/rh.entorhinal_exvivo.stats ]; then
echo "--- SKIPPING: {TEMPLATEID} sentinal file already exits: {FSSUBJDIR}/{TEMPLATEID}/stats/rh.entorhinal_exvivo.stats"
status=$?
else
{FSHOME}/bin/recon-all -debug -base {TEMPLATEID} {ALL_TIME_POINTS}
status=$?
fi
exit $status
""".format(SOURCE_SCRIPT=FS_SCRIPT_FN,
FSHOME=FREESURFER_HOME,
FSSUBJDIR=subjects_dir,
TEMPLATEID=base_template_id,
ALL_TIME_POINTS=allTimePointFlags)
base_run_dir = os.path.join(subjects_dir, base_template_id, 'scripts')
mkdir_p(base_run_dir)
script_name = os.path.join(base_run_dir,'run_autorecon_stage_'+str(StageToRun)+'.sh')
script = open(script_name, 'w')
script.write(auto_recon_script)
script.close()
os.chmod(script_name, 0777)
script_name_stdout = script_name + '_out'
script_name_stdout_fid = open(script_name_stdout, 'w')
print "Starting auto_recon Stage: {0} for SubjectSession {1}".format(StageToRun, base_template_id)
scriptStatus = subprocess.check_call([script_name], stdout=script_name_stdout_fid, stderr=subprocess.STDOUT, shell='/bin/bash')
if scriptStatus != 0:
sys.exit(scriptStatus)
print "Ending auto_recon Stage: {0} for SubjectSession {1}".format(StageToRun, base_template_id)
script_name_stdout_fid.close()
return
def runLongitudinal(args, FREESURFER_HOME, FS_SCRIPT):
""" Create the longitudinal analysis """
subj_session_id = args.subj_session_id
subjects_dir = args.subjects_dir
base_template_id = args.base_template_id
assert isinstance(subj_session_id, str), "Must input a singel subj_session_id as string :{0}:".format(subj_session_id)
StageToRun = "Longitudinal"
FS_SCRIPT_FN = os.path.join(FREESURFER_HOME, FS_SCRIPT)
auto_recon_script = """#!/bin/bash
#$ -o {FSSUBJDIR}/{LONGSESSIONID}/scripts/long_{TEMPLATEID}_{LONGSESSIONID}_qsub.out
#$ -e {FSSUBJDIR}/{LONGSESSIONID}/scripts/long_{TEMPLATEID}_{LONGSESSIONID}_qsub.err
#$ -cwd
export FREESURFER_HOME={FSHOME}
export SUBJECTS_DIR={FSSUBJDIR}
source {SOURCE_SCRIPT}
## Need to delete the "IsRunning" flags, if nipype pipeline is running this, then nipype prevents duplicates
rm -f {FSSUBJDIR}/{LONGSESSIONID}/scripts/Is*
if [ -f {FSSUBJDIR}/{LONGSESSIONID}.long.{TEMPLATEID}/stats/rh.entorhinal_exvivo.stats ]; then
echo "--- SKIPPING: {LONGSESSIONID}.long.{TEMPLATEID} file already exits: {FSSUBJDIR}/{LONGSESSIONID}.long.{TEMPLATEID}/stats/rh.entorhinal_exvivo.stats"
status=$?
else
echo "--- RUNNING: {LONGSESSIONID}.long.{TEMPLATEID} file already exits: {FSSUBJDIR}/{LONGSESSIONID}.long.{TEMPLATEID}/stats/rh.entorhinal_exvivo.stats"
{FSHOME}/bin/recon-all -debug -long {LONGSESSIONID} {TEMPLATEID} -all
status=$?
fi
exit $status
""".format(SOURCE_SCRIPT=FS_SCRIPT_FN,
FSHOME=FREESURFER_HOME,
FSSUBJDIR=subjects_dir,
TEMPLATEID=base_template_id,
LONGSESSIONID=subj_session_id)
base_run_dir = os.path.join(subjects_dir, subj_session_id, 'scripts')
mkdir_p(base_run_dir)
script_name = os.path.join(base_run_dir,'run_autorecon_stage_'+str(StageToRun)+'.sh')
script = open(script_name, 'w')
script.write(auto_recon_script)
script.close()
os.chmod(script_name, 0777)
script_name_stdout = script_name + '_out'
script_name_stdout_fid = open(script_name_stdout, 'w')
print "Starting auto_recon Stage: {0} for SubjectSession {1}".format(StageToRun, base_template_id)
scriptStatus = subprocess.check_call([script_name], stdout=script_name_stdout_fid, stderr=subprocess.STDOUT, shell='/bin/bash')
if scriptStatus != 0:
sys.exit(scriptStatus)
print "Ending auto_recon Stage: {0} for SubjectSession {1}".format(StageToRun, base_template_id)
script_name_stdout_fid.close()
return
def runAutoRecon(args, FREESURFER_HOME, FS_SCRIPT):
"""Run all stages of AutoRecon For FreeSurfer, including the custom BAW initialization."""
runAutoReconStage(args.subj_session_id, 1, args.T1_files, args.subjects_dir, FREESURFER_HOME, FS_SCRIPT)
baw_FixBrainMask(args.brainmask, args.subjects_dir, FREESURFER_HOME, FS_SCRIPT, args.subj_session_id)
runAutoReconStage(args.subj_session_id, 2, args.T1_files, args.subjects_dir, FREESURFER_HOME, FS_SCRIPT)
runAutoReconStage(args.subj_session_id, 3, args.T1_files, args.subjects_dir, FREESURFER_HOME, FS_SCRIPT)
dirname = os.path.join(args.subjects_dir, args.subj_session_id)
t1 = os.path.join(dirname, 'mri', 'brain.mgz')
label1 = os.path.join(dirname, 'mri_nifti', 'aparc+aseg.nii.gz')
label2 = os.path.join(dirname, 'mri_nifti', 'aparc.a2009+aseg.nii.gz')
return t1, label1, label2, args.subj_session_id
if __name__ == "__main__":
parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter,
description="""
Run various FreeSurfer's recon-all methods
""", epilog="""
For more information:
---------------------
* http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
* http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags
""")
## For the current nipype processing, the environments are set prior to running this script, so this code is not
## needed for using this script within the baw running envirionment.
# TODO: Make parser group "Environment"
# TODO: parser.add_argument('--FSHomeDir', action='store', dest='FREESURFER_HOME',
# TODO: default='/ipldev/sharedopt/20110601/MacOSX_10.6/freesurfer',
# TODO: help='Location of FreeSurfer (differs for Mac and Linux environments')
# TODO: parser.add_argument('--FSSource', action='store', dest='FS_SCRIPT',
# TODO: default='FreeSurferEnv.sh', help='')
# TODO: local_FREESURFER_HOME = all_args.FREESURFER_HOME
# TODO: local_FS_SCRIPT = all_args.FS_SCRIPT
### HACK:
try:
local_FREESURFER_HOME = os.environ['FREESURFER_HOME']
if not os.path.exists(local_FREESURFER_HOME):
raise Exception("INVALID PATH FOR FREESURFER HOME :{0}:".format(local_FREESURFER_HOME))
# local_FS_SCRIPT = os.path.join(local_FREESURFER_HOME,'FreeSurferEnv.sh')
local_FS_SCRIPT = 'FreeSurferEnv.sh'
except KeyError, err:
print KeyError
print err
raise KeyError
### END HACK
subparsers = parser.add_subparsers(help='Currently supported subprocesses: "autorecon", "template", "longitudinal"')
# Create -make subparser
autorecon = subparsers.add_parser('autorecon', help='Link to recon-all i/o table: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable')
autorecon.add_argument('--subjects_dir', action='store', dest='subjects_dir', help='FreeSurfer subjects directory')
autorecon.add_argument('--subj_session_id', action='store', dest='subj_session_id', required=True, help='Subject_Session')
autorecon.add_argument('--T1_files', action='store', dest='T1_files', required=True, help='Original T1 image')
autorecon.add_argument('--brainmask', action='store', dest='brainmask', required=True,
help='The normalized T1 image with the skull removed. Normalized 0-110 where white matter=110.')
autorecon.set_defaults(func=runAutoRecon)
# Create -base subparser
template = subparsers.add_parser('template', help='Link to recon-all longitudinal processing: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing')
template.add_argument('--subjects_dir', action='store', dest='subjects_dir',required=True, help='FreeSurfer subjects directory')
template.add_argument('--base_template_id', action='store', dest='base_template_id', required=True, help='Subject_template')
template.add_argument('--list_all_subj_session_ids', action='store', dest='list_all_subj_session_ids', nargs='+', required=True, help='List of sessions for a subject template')
template.set_defaults(func=runSubjectTemplate)
# Create -long subparser
longitudinal = subparsers.add_parser('longitudinal', help='Link to recon-all longitudinal processing: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing')
longitudinal.add_argument('--subjects_dir', action='store', dest='subjects_dir', required=True, help='FreeSurfer subjects directory')
longitudinal.add_argument('--subj_session_id', action='store', dest='subj_session_id', required=True, help='Subject_Session')
longitudinal.add_argument('--base_template_id', action='store', dest='base_template_id', required=True, help='Template folder name (--base_template_id from "template" option)')
longitudinal.set_defaults(func=runLongitudinal)
# Parse inputs and run correct function
all_args = parser.parse_args()
all_args.func(all_args, local_FREESURFER_HOME, local_FS_SCRIPT)