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 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 $status
""".format(SOURCE_SCRIPT=FS_SCRIPT_FN,
FSHOME=FREESURFER_HOME,
FSSUBJDIR=subjects_dir,
TEMPLATEID=base_template_id,
LONGSESSIONID=subj_session_id)
base_run_dir = os.path.join(subjects_dir, subj_session_id, 'scripts')
mkdir_p(base_run_dir)
script_name = os.path.join(
base_run_dir, 'run_autorecon_stage_' + str(StageToRun) + '.sh')
script = open(script_name, 'w')
script.write(auto_recon_script)
script.close()
os.chmod(script_name, 0777)
script_name_stdout = script_name + '_out'
script_name_stdout_fid = open(script_name_stdout, 'w')
print "Starting auto_recon Stage: {0} for SubjectSession {1}".format(
StageToRun, base_template_id)
scriptStatus = subprocess.check_call([script_name],
stdout=script_name_stdout_fid,
stderr=subprocess.STDOUT,
shell='/bin/bash')
if scriptStatus != 0:
sys.exit(scriptStatus)
print "Ending auto_recon Stage: {0} for SubjectSession {1}".format(
StageToRun, base_template_id)
script_name_stdout_fid.close()
return
def runSubjectTemplate(args, FREESURFER_HOME, FS_SCRIPT):
""" Create the within-subject template """
base_template_id = args.base_template_id
list_all_subj_session_ids = args.list_all_subj_session_ids
subjects_dir = args.subjects_dir
print "X" * 80
print "base_template_id :{0}:".format(base_template_id)
print "Input a list of list_all_subj_session_ids :{0}:".format(list_all_subj_session_ids)
print "subjects_dir :{0}:".format(subjects_dir)
print "X" * 80
assert isinstance(list_all_subj_session_ids, list), "Must input a list of list_all_subj_session_ids :{0}:".format(list_all_subj_session_ids)
StageToRun = "Within-SubjectTemplate"
FS_SCRIPT_FN = os.path.join(FREESURFER_HOME, FS_SCRIPT)
allTimePointFlags = ""
for subj_session_id in list_all_subj_session_ids:
allTimePointFlags += " -tp {timepoint}".format(timepoint=subj_session_id)
allTimePointFlags += " -all"
auto_recon_script = """#!/bin/bash
#$ -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 $status
""".format(SOURCE_SCRIPT=FS_SCRIPT_FN,
FSHOME=FREESURFER_HOME,
FSSUBJDIR=subjects_dir,
TEMPLATEID=base_template_id,
ALL_TIME_POINTS=allTimePointFlags)
base_run_dir = os.path.join(subjects_dir, base_template_id, 'scripts')
mkdir_p(base_run_dir)
script_name = os.path.join(base_run_dir, 'run_autorecon_stage_' + str(StageToRun) + '.sh')
script = open(script_name, 'w')
script.write(auto_recon_script)
script.close()
os.chmod(script_name, 0777)
script_name_stdout = script_name + '_out'
script_name_stdout_fid = open(script_name_stdout, 'w')
print "Starting auto_recon Stage: {0} for SubjectSession {1}".format(StageToRun, base_template_id)
scriptStatus = subprocess.check_call([script_name], stdout=script_name_stdout_fid, stderr=subprocess.STDOUT, shell='/bin/bash')
if scriptStatus != 0:
sys.exit(scriptStatus)
print "Ending auto_recon Stage: {0} for SubjectSession {1}".format(StageToRun, base_template_id)
script_name_stdout_fid.close()
return
def runAutoReconStage(subj_session_id, StageToRun, t1_fn, subjects_dir,
FREESURFER_HOME, FS_SCRIPT):
FS_SCRIPT_FN = os.path.join(FREESURFER_HOME, FS_SCRIPT)
base_subj_dir = os.path.join(subjects_dir, subj_session_id)
orig_001_mgz_fn = os.path.join(base_subj_dir, 'mri', 'orig', '001.mgz')
if IsFirstNewerThanSecond(t1_fn, orig_001_mgz_fn):
if os.path.exists(base_subj_dir):
removeDir(base_subj_dir)
mkdir_p(os.path.dirname(orig_001_mgz_fn))
run_mri_convert_script(t1_fn, orig_001_mgz_fn, subjects_dir,
subj_session_id, FREESURFER_HOME, FS_SCRIPT)
auto_recon_script = """#!/bin/bash
#$ -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 $status
""".format(SOURCE_SCRIPT=FS_SCRIPT_FN,
FSHOME=FREESURFER_HOME,
FSSUBJDIR=subjects_dir,
AUTORECONSTAGE=StageToRun,
SUBJ_SESSION_ID=subj_session_id)
base_run_dir = os.path.join(subjects_dir, subj_session_id, 'scripts')
mkdir_p(base_run_dir)
script_name = os.path.join(base_run_dir,
'run_autorecon_stage' + str(StageToRun) + '.sh')
script = open(script_name, 'w')
script.write(auto_recon_script)
script.close()
os.chmod(script_name, 0777)
script_name_stdout = script_name + '_out'
script_name_stdout_fid = open(script_name_stdout, 'w')
print "Starting auto_recon Stage: {0} for SubjectSession {1}".format(
StageToRun, subj_session_id)
scriptStatus = subprocess.check_call([script_name],
stdout=script_name_stdout_fid,
stderr=subprocess.STDOUT,
shell='/bin/bash')
if scriptStatus != 0:
sys.exit(scriptStatus)
print "Ending auto_recon Stage: {0} for SubjectSession {1}".format(
StageToRun, subj_session_id)
script_name_stdout_fid.close()
return
def runLongitudinal(args, FREESURFER_HOME, FS_SCRIPT):
""" Create the longitudinal analysis """
subj_session_id = args.subj_session_id
subjects_dir = args.subjects_dir
base_template_id = args.base_template_id
assert isinstance(subj_session_id, str), "Must input a singel subj_session_id as string :{0}:".format(subj_session_id)
StageToRun = "Longitudinal"
FS_SCRIPT_FN = os.path.join(FREESURFER_HOME, FS_SCRIPT)
auto_recon_script = """#!/bin/bash
#$ -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 $status
""".format(SOURCE_SCRIPT=FS_SCRIPT_FN,
FSHOME=FREESURFER_HOME,
FSSUBJDIR=subjects_dir,
TEMPLATEID=base_template_id,
LONGSESSIONID=subj_session_id)
base_run_dir = os.path.join(subjects_dir, subj_session_id, 'scripts')
mkdir_p(base_run_dir)
script_name = os.path.join(base_run_dir, 'run_autorecon_stage_' + str(StageToRun) + '.sh')
script = open(script_name, 'w')
script.write(auto_recon_script)
script.close()
os.chmod(script_name, 0777)
script_name_stdout = script_name + '_out'
script_name_stdout_fid = open(script_name_stdout, 'w')
print "Starting auto_recon Stage: {0} for SubjectSession {1}".format(StageToRun, base_template_id)
scriptStatus = subprocess.check_call([script_name], stdout=script_name_stdout_fid, stderr=subprocess.STDOUT, shell='/bin/bash')
if scriptStatus != 0:
sys.exit(scriptStatus)
print "Ending auto_recon Stage: {0} for SubjectSession {1}".format(StageToRun, base_template_id)
script_name_stdout_fid.close()
return
def runSubjectTemplate(args, FREESURFER_HOME, FS_SCRIPT):
""" Create the within-subject template """
subjectTemplate_id = args.subjectTemplate_id
session_ids = args.session_ids
subjects_dir = args.subjects_dir
print "X"*80
print "subjectTemplate_id :{0}:".format(subjectTemplate_id)
print "Input a list of session_ids :{0}:".format(session_ids)
print "subjects_dir :{0}:".format(subjects_dir)
print "X"*80
assert isinstance(session_ids, list), "Must input a list of session_ids :{0}:".format(session_ids)
StageToRun = "Within-SubjectTemplate"
FS_SCRIPT_FN = os.path.join(FREESURFER_HOME, FS_SCRIPT)
allTimePointFlags = ""
for session_id in session_ids:
allTimePointFlags += " -tp {timepoint}".format(timepoint=session_id)
allTimePointFlags += " -all"
auto_recon_script="""#!/bin/bash
export FREESURFER_HOME={FSHOME}
export SUBJECTS_DIR={FSSUBJDIR}
source {SOURCE_SCRIPT}
{FSHOME}/bin/recon-all -debug -base {TEMPLATEID} {ALL_TIME_POINTS}
status=$?
exit $status
""".format(SOURCE_SCRIPT=FS_SCRIPT_FN,
FSHOME=FREESURFER_HOME,
FSSUBJDIR=subjects_dir,
TEMPLATEID=subjectTemplate_id,
ALL_TIME_POINTS=allTimePointFlags)
base_run_dir = os.path.join(subjects_dir,'run_scripts', subjectTemplate_id)
mkdir_p(base_run_dir)
script_name = os.path.join(base_run_dir,'run_autorecon_stage_'+str(StageToRun)+'.sh')
script = open(script_name, 'w')
script.write(auto_recon_script)
script.close()
os.chmod(script_name, 0777)
script_name_stdout = script_name + '_out'
script_name_stdout_fid = open(script_name_stdout, 'w')
print "Starting auto_recon Stage: {0} for SubjectSession {1}".format(StageToRun, subjectTemplate_id)
scriptStatus = subprocess.check_call([script_name], stdout=script_name_stdout_fid, stderr=subprocess.STDOUT, shell='/bin/bash')
if scriptStatus != 0:
sys.exit(scriptStatus)
print "Ending auto_recon Stage: {0} for SubjectSession {1}".format(StageToRun, subjectTemplate_id)
script_name_stdout_fid.close()
return
def runAutoReconStage(subj_session_id, StageToRun, t1_fn, subjects_dir, FREESURFER_HOME, FS_SCRIPT):
FS_SCRIPT_FN = os.path.join(FREESURFER_HOME, FS_SCRIPT)
base_subj_dir = os.path.join(subjects_dir, subj_session_id)
orig_001_mgz_fn = os.path.join(base_subj_dir, 'mri', 'orig', '001.mgz')
if IsFirstNewerThanSecond(t1_fn, orig_001_mgz_fn):
if os.path.exists(base_subj_dir):
removeDir(base_subj_dir)
mkdir_p(os.path.dirname(orig_001_mgz_fn))
run_mri_convert_script(t1_fn, orig_001_mgz_fn, subjects_dir, subj_session_id, FREESURFER_HOME, FS_SCRIPT)
auto_recon_script = """#!/bin/bash
#$ -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 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 runLongitudinal(args, FREESURFER_HOME, FS_SCRIPT):
""" Create the longitudinal analysis """
session_id = args.session_id
subjects_dir = args.subjects_dir
template_id = args.template_id
assert type(session_id, str), "Must input a list of session_ids"
StageToRun = "Longitudinal"
FS_SCRIPT_FN = os.path.join(FREESURFER_HOME, FS_SCRIPT)
auto_recon_script = """#!/bin/bash
export FREESURFER_HOME={FSHOME}
export SUBJECTS_DIR={FSSUBJDIR}
source {SOURCE_SCRIPT}
{FSHOME}/bin/recon-all -debug -long {TIMEPOINT} {TEMPLATEID} -all
status=$?
mv -n {FSSUBJDIR}/{TIMEPOINT}.long.{TEMPLATEID} {FSSUBJDIR}/{TEMPLATEID}_{TIMEPOINT}.long
exit $status
""".format(SOURCE_SCRIPT=FS_SCRIPT_FN,
FSHOME=FREESURFER_HOME,
FSSUBJDIR=subjects_dir,
TEMPLATEID=template_id,
TIMEPOINT=session_id)
base_run_dir = os.path.join(subjects_dir,'run_scripts', template_id)
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, 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, template_id)
script_name_stdout_fid.close()
return
def runSubjectTemplate(args, FREESURFER_HOME, FS_SCRIPT):
import sys
""" 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 = ""
## Determine if previous run had same sessions as current run
base_tempate_list = os.path.join(subjects_dir, base_template_id,
'base-tps')
#print "XXX Setting file to look for ", base_tempate_list
prev_sessions = list()
if os.path.exists(base_tempate_list):
#print "XXX Opening ", base_tempate_list
ff = open(base_tempate_list, 'r')
#print "XXX Reading lines"
prev_sessions = ff.readlines()
#print prev_sessions
prev_sessions = [x.rstrip() for x in prev_sessions]
#print prev_sessions
reset_template_directory = False
for subj_session_id in list_all_subj_session_ids:
allTimePointFlags += " -tp {timepoint}".format(
timepoint=subj_session_id)
if subj_session_id not in prev_sessions:
reset_template_directory = True
#print("XXXXXXXXXXX {0} =? {1}".format(prev_sessions,list_all_subj_session_ids))
#print("XXXX {0}".format(reset_template_directory))
if reset_template_directory:
recursive_dir_rm(os.path.join(subjects_dir, base_template_id))
## Now remove subsequent directories
for subj_session_id in list_all_subj_session_ids:
recursive_dir_rm(
os.path.join(subjects_dir,
subj_session_id + '.long.' + base_template_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 runSubjectTemplate(args, FREESURFER_HOME, FS_SCRIPT):
import sys
""" 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 = ""
## Determine if previous run had same sessions as current run
base_tempate_list = os.path.join(subjects_dir,base_template_id,'base-tps')
#print "XXX Setting file to look for ", base_tempate_list
prev_sessions = list()
if os.path.exists(base_tempate_list):
#print "XXX Opening ", base_tempate_list
ff = open ( base_tempate_list, 'r' )
#print "XXX Reading lines"
prev_sessions = ff.readlines()
#print prev_sessions
prev_sessions = [ x.rstrip() for x in prev_sessions ]
#print prev_sessions
reset_template_directory = False
for subj_session_id in list_all_subj_session_ids:
allTimePointFlags += " -tp {timepoint}".format(timepoint=subj_session_id)
if subj_session_id not in prev_sessions:
reset_template_directory = True
#print("XXXXXXXXXXX {0} =? {1}".format(prev_sessions,list_all_subj_session_ids))
#print("XXXX {0}".format(reset_template_directory))
if reset_template_directory:
recursive_dir_rm(os.path.join(subjects_dir,base_template_id))
## Now remove subsequent directories
for subj_session_id in list_all_subj_session_ids:
recursive_dir_rm(os.path.join(subjects_dir,subj_session_id+'.long.'+base_template_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 $status
""".format(SOURCE_SCRIPT=FS_SCRIPT_FN,
FSHOME=FREESURFER_HOME,
FSSUBJDIR=subjects_dir,
TEMPLATEID=base_template_id,
ALL_TIME_POINTS=allTimePointFlags)
base_run_dir = os.path.join(subjects_dir, base_template_id, 'scripts')
mkdir_p(base_run_dir)
script_name = os.path.join(base_run_dir, 'run_autorecon_stage_' + str(StageToRun) + '.sh')
script = open(script_name, 'w')
script.write(auto_recon_script)
script.close()
os.chmod(script_name, 0777)
script_name_stdout = script_name + '_out'
script_name_stdout_fid = open(script_name_stdout, 'w')
print "Starting auto_recon Stage: {0} for SubjectSession {1}".format(StageToRun, base_template_id)
scriptStatus = subprocess.check_call([script_name], stdout=script_name_stdout_fid, stderr=subprocess.STDOUT, shell='/bin/bash')
if scriptStatus != 0:
sys.exit(scriptStatus)
print "Ending auto_recon Stage: {0} for SubjectSession {1}".format(StageToRun, base_template_id)
script_name_stdout_fid.close()
return
def runSubjectTemplate(args, FREESURFER_HOME, FS_SCRIPT):
""" Create the within-subject template """
base_template_id = args.base_template_id
list_all_subj_session_ids = args.list_all_subj_session_ids
subjects_dir = args.subjects_dir
print "X" * 80
print "base_template_id :{0}:".format(base_template_id)
print "Input a list of list_all_subj_session_ids :{0}:".format(
list_all_subj_session_ids)
print "subjects_dir :{0}:".format(subjects_dir)
print "X" * 80
assert isinstance(
list_all_subj_session_ids,
list), "Must input a list of list_all_subj_session_ids :{0}:".format(
list_all_subj_session_ids)
StageToRun = "Within-SubjectTemplate"
FS_SCRIPT_FN = os.path.join(FREESURFER_HOME, FS_SCRIPT)
allTimePointFlags = ""
for subj_session_id in list_all_subj_session_ids:
allTimePointFlags += " -tp {timepoint}".format(
timepoint=subj_session_id)
allTimePointFlags += " -all"
auto_recon_script = """#!/bin/bash
#$ -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