Commit 955bf978 authored by Christoph Arthofer's avatar Christoph Arthofer
Browse files

Changed masking to mean and threshold to 0.5

parent 2f0be14e
......@@ -17,12 +17,11 @@ import sys
from fsl.wrappers import fslmaths,flirt,applyxfm,concatxfm,bet,fast,fslstats
from fsl.wrappers.fnirt import invwarp, applywarp, convertwarp
from file_tree import FileTree
from fsl.utils.fslsub import func_to_cmd
from operator import itemgetter
import tempfile
import argparse
from fsl.utils.fslsub import func_to_cmd
import fsl_sub
import logging
def writeConfig(step,mod,fpath):
"""! Writes the nonlinear registration parameters for a given resolution level and modalities to a file readable by MMORF.
......@@ -535,19 +534,19 @@ def submitJob(command, name, log_dir, queue, wait_for=None, array_task=False, co
hold_ids.append(job_id)
job_id = fsl_sub.submit(command=command,
array_task=array_task,
jobhold=hold_ids,
name=name,
logdir=log_dir,
queue=queue,
coprocessor=coprocessor,
coprocessor_class=coprocessor_class,
coprocessor_class_strict=coprocessor_class_strict,
coprocessor_multi=coprocessor_multi,
threads=threads,
export_vars=export_var,
jobram=jobram,
jobtime=jobtime
array_task=array_task,
jobhold=hold_ids,
name=name,
logdir=log_dir,
queue=queue,
coprocessor=coprocessor,
coprocessor_class=coprocessor_class,
coprocessor_class_strict=coprocessor_class_strict,
coprocessor_multi=coprocessor_multi,
threads=threads,
export_vars=export_var,
jobram=jobram,
jobtime=jobtime
)
return str(job_id)
......@@ -814,8 +813,6 @@ def mmorfWrapper(mmorf_run_cmd, config_path, img_warp_space,
if __name__ == "__main__":
"""! Main function submitting the jobs.
"""
logging.basicConfig()
logging.getLogger('fsl.wrappers').setLevel(logging.DEBUG)
mni_path = os.getenv('FSLDIR')+'/data/standard/MNI152lin_T1_1mm_brain.nii.gz'
identity_path = os.getenv('FSLDIR')+'/etc/flirtsch/ident.mat'
......@@ -900,7 +897,7 @@ if __name__ == "__main__":
jobram_low = 4
jobram_hi = 12
jobtime_low = 15
jobtime_low = 20
jobtime_high = 60
job_ids = ['' for _ in range(100)]
......@@ -955,7 +952,7 @@ if __name__ == "__main__":
tree = tree.update(sub_id=id)
T1_head_path = tree.get(mod['T1_head_key'])
T1_clamped_path = tree.get('T1_head_clamped', make_dir=True)
T1_clamped_hard_path = tree.get('T1_head_clamped_hard')
T1_clamped_hard_path = tree.get('T1_head_clamped_hard', make_dir=True)
jobcmd = func_to_cmd(run_soft_clamp,
args=(T1_head_path, T1_clamped_path),
......@@ -1305,7 +1302,7 @@ if __name__ == "__main__":
print('submitted: ' + task_name)
task_name = '{:03d}_affT_create_weighted_brain_mask'.format(task_count)
jobcmd = 'fslmaths ' + aff_template_path + ' -thr 0.1 -bin -mul 7 -add 1 -inm 1 ' + tree.get('T1_brain_mask_weighted_affine_template')
jobcmd = 'fslmaths ' + aff_template_path + ' -thr 0.5 -bin -mul 7 -add 1 -inm 1 ' + tree.get('T1_brain_mask_weighted_affine_template')
# job_ids[23] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[22]])
job_ids[23] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq, wait_for=[job_ids[22]], array_task=False, jobram=jobram_low, jobtime=jobtime_low)
print('submitted: ' + task_name)
......@@ -1854,7 +1851,7 @@ if __name__ == "__main__":
img_paths.append(tree.get('warped_T1brain_mask'))
nln_template_path = tree.get('T1_brain_mask_nln_template')
jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, 'intersection', False), tmp_dir=script_dir,
jobcmd = func_to_cmd(averageImages, args=(img_paths, nln_template_path, 'mean', False), tmp_dir=script_dir,
kwargs=None, clean="never")
# job_ids[49] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[38]])
job_ids[49] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq, wait_for=[job_ids[38]], array_task=False, jobram=jobram_low, jobtime=jobtime_low)
......@@ -1862,7 +1859,7 @@ if __name__ == "__main__":
task_count += 1
task_name = '{:03d}_nlnT_average_T1_brain_mask_weighted'.format(task_count)
jobcmd = 'fslmaths ' + nln_template_path + ' -thr 0.1 -bin -mul 7 -add 1 -inm 1 ' + tree.get(
jobcmd = 'fslmaths ' + nln_template_path + ' -thr 0.5 -bin -mul 7 -add 1 -inm 1 ' + tree.get(
'T1_brain_mask_weighted_nln_template')
# job_ids[50] = submitJob(tag+'_'+task_name, log_dir, command=jobcmd, queue=cpuq, wait_for=[job_ids[49]])
job_ids[50] = submitJob(jobcmd, tag + '_' + task_name, log_dir, queue=cpuq, wait_for=[job_ids[49]], array_task=False, jobram=jobram_low, jobtime=jobtime_low)
......
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