def run_hippocampal_segmentation(project_id, subject_id, view, hemisphere):
''' Run External Surface Segmentation from ENIGMA cortical pipeline'''
local_fs = './freesurfer/' + subject_id
output_path = './freesurfer/QC'
current_files = glob.glob(output_path + '/' + subject_id + '/*.png')
datetime_start = datetime.datetime.now()
# Run segmentation
if not os.path.exists(local_fs):
print("%s: ERROR: Didn't find FreeSurfer output for %s subject. Please run run_freesurfer function first." (datetime_start,subject_id))
else:
print("%s: Getting External Surface Segmentation for %s subject..." % (str(datetime_start), subject_id))
if len(current_files) > 1:
datetime_end = datetime.datetime.now()
print("%s: External Surface Segmentation was already obtained for %s subject." % (str(datetime_end),subject_id))
else:
cmd = ['/bin/bash', './scripts/QC_subfields_step_1_prepare_extension.sh', subject_id, output_path]
output = utils.run_command(cmd)
cmd = ['octave-cli', '/NIfTI/QC_subfields_step_2_prepare_extension']
output = utils.run_command(cmd)
datetime_end = datetime.datetime.now()
print("%s: Segmentation FINISHED (Total time: %s)." % (str(datetime_end), str(datetime_end-datetime_start)))
datetime_plot = str(datetime.datetime.now())
print("%s: Visualizing results:" % (datetime_plot))
get_hippocampal_qc(project_id, subject_id, current_files, view, hemisphere)
def extract_hippocampal_measures(project_id, subject_id):
''' Run Hippocampal Measures Extraction for ENIGMA Hippocampal pipeline'''
subject_path = './freesurfer'
local_output = subject_path + '/' + subject_id
datetime_start = datetime.datetime.now()
# Run Hippocampal measures extraction
if not os.path.exists(local_output):
print(
"%s: ERROR: Didn't find FreeSurfer output for %s subject. Please run run_freesurfer function first."
)(datetime_start, subject_id)
else:
print("%s: Extracting hippocampal measures for %s subject..." %
(str(datetime_start), subject_id))
output_file = './results/' + project_id + '/hippo_' + subject_id + '.csv'
cmd = [
'/bin/bash', './scripts/extract_subfields.sh', subject_id,
subject_path, output_file
]
output = utils.run_command(cmd)
datetime_end = datetime.datetime.now()
print("%s: Extraction FINISHED (Total time: %s)." %
(str(datetime_end), str(datetime_end - datetime_start)))
return output_file
def run_freesurfer_hippocampal(project_id, subject_id, mri_type = "T1-weighted"):
''' Run FreeSurfer for ENIGMA Hippocampal pipeline'''
# Query data
query_txt = """query {
mri_exam(project_id: "%s", scan_type: "%s", with_path_to:{type:"case", submitter_id:"%s"}){
mri_images{
file_name
id
}
}
}""" % (project_id, mri_type, subject_id)
data = query_api(query_txt)
# Get file from S3
filename = data['data']['mri_exam'][0]['mri_images'][0]['file_name']
fileid = data['data']['mri_exam'][0]['mri_images'][0]['file_name']
localpath = utils.download_file(auth, api_url, fileid, filename)
# Run freesurfer
datetime_start = datetime.datetime.now()
print("%s: Running FreeSurfer for %s subject..." % (str(datetime_start),subject_id))
local_output = './freesurfer/' + subject_id
if not os.path.exists(local_output):
cmd = ['/bin/bash', './scripts/run_freesurfer_hippocampal.sh', subject_id, localpath]
output = utils.run_command(cmd)
datetime_end = datetime.datetime.now()
print("%s: Hippocampal FreeSurfer FINISHED (Total time: %s)." % (str(datetime_end), str(datetime_end-datetime_start)))
else:
print("%s: Hippocampal FreeSurfer results were already found for %s subject." % (str(datetime_start), subject_id))
def run_external_segmentation(project_id, subject_id):
''' Run External Surface Segmentation from ENIGMA cortical pipeline'''
local_fs = './freesurfer/' + subject_id
output_path = './results/' + project_id
current_files = glob.glob(output_path + '/' + subject_id + '*.tif')
datetime_start = datetime.datetime.now()
# Run segmentation
if not os.path.exists(local_fs):
print("%s: ERROR: Didn't find FreeSurfer output for %s subject. Please run run_freesurfer function first." (datetime_start,subject_id))
else:
print("%s: Getting External Surface Segmentation for %s subject..." % (str(datetime_start), subject_id))
if len(current_files) > 1:
datetime_end = datetime.datetime.now()
print("%s: Segmentation FINISHED: External Surface Segmentation was already obtained for %s subject." % (str(datetime_end),subject_id))
else:
cmd = ['/bin/bash', './scripts/fsqc.sh', subject_id, output_path]
output = utils.run_command(cmd)
datetime_end = datetime.datetime.now()
print("%s: Segmentation FINISHED (Total time: %s)." % (str(datetime_end), str(datetime_end-datetime_start)))
datetime_plot = str(datetime.datetime.now())
print("%s: Visualizing results:" % (datetime_plot))
get_external_surface_qc(project_id, subject_id)
def extract_cortical_measures(project_id, subject_id):
''' Run Cortical Measures Extraction for ENIGMA cortical pipeline'''
subject_path = './freesurfer'
local_output = subject_path + '/' + subject_id
datetime_start = datetime.datetime.now()
# Run Cortical measures extraction
if not os.path.exists(local_output):
print(
"%s: ERROR: Didn't find FreeSurfer output for %s subject. Please run run_freesurfer function first."
)(datetime_start, subject_id)
else:
resultDir_forProject = './results/' + project_id
if not os.path.exists(resultDir_forProject):
os.system('mkdir -p ' + resultDir_forProject)
print("%s: Extracting cortical measures for %s subject..." %
(str(datetime_start), subject_id))
#output_thickAvg = resultDir_forProject + '/cort_' + subject_id + '_thickAvg.csv'
#output_surfAvg = resultDir_forProject + '/cort_' + subject_id + '_surfAvg.csv'
#os.makedirs(os.path.dirname(output_thickAvg))
#os.makedirs(os.path.dirname(output_surfAvg))
output_thickAvg = '/home/jovyan/pd/demos/ENIGMA_Cortical_Thickness/results/' + project_id + '/cort_' + subject_id + '_thickAvg.csv'
output_surfAvg = '/home/jovyan/pd/demos/ENIGMA_Cortical_Thickness/results/' + project_id + '/cort_' + subject_id + '_surfAvg.csv'
cmd = [
'/bin/bash', './extract_singleSubject.sh', subject_id,
subject_path, output_thickAvg, output_surfAvg
]
output = utils.run_command(cmd)
datetime_end = datetime.datetime.now()
print("%s: Extraction FINISHED (Total time: %s)." %
(str(datetime_end), str(datetime_end - datetime_start)))
return output_thickAvg, output_surfAvg