def process_subject_anatomy(t1):
reconall = ReconAll()
reconall.inputs.subject_id = t1.split('/')[-3]
reconall.inputs.directive = 'all'
reconall.inputs.subjects_dir = subjects_dir
reconall.inputs.T1_files = t1
reconall.run()
def process_subject_anatomy(subject, t1, subjects_dir='/cluster/transcend/MRI/WMA/recons'):
reconall = ReconAll()
reconall.inputs.subject_id = subject
reconall.inputs.directive = 'all'
reconall.inputs.subjects_dir = subjects_dir
reconall.inputs.T1_files = t1
reconall.run()
def run_recon_all(subject=None, subjects_dir=subjects_dir, openmp=1):
reconall = ReconAll()
if not os.path.isdir(subjects_dir):
print(
f"Subjects directory {subjects_dir} does not exist, creating it.")
os.mkdir(subjects_dir)
if not os.path.isdir(os.path.join(subjects_dir, subject, "mri")):
anafolder = os.path.join(args.folder, subject)
# catch error, if no .nii exists
try:
nii_file = glob.glob(anafolder + "/*.nii*")[0]
reconall.inputs.subject_id = subject
reconall.inputs.T1_files = nii_file
reconall.inputs.directive = 'all'
reconall.inputs.subjects_dir = subjects_dir
reconall.inputs.openmp = openmp
reconall.inputs.flags = "-3T"
print(f"Now running recon-all for subject {subject}")
print(f".nii-file used was: {nii_file}")
reconall.run()
except Exception as e:
print(e)
else:
print(
f"A freesurfer segmentation of subject {subject} already exists in {subjects_dir} - aborting"
)
def _nii_to_freesurfer(self):
reconall = ReconAll()
if not self.subject.startswith("sub-"):
self.subject = "sub-" + self.subject
# check if freesurfer segmentation was already performed
freesurfered = os.path.join(self.FS_SUBJECTS_DIR, self.subject)
if not os.path.isdir(freesurfered):
nii_file = glob.glob(opj(self.mri_folder, "*.nii*"))[0]
reconall.inputs.subject_id = self.subject
reconall.inputs.T1_files = nii_file
reconall.inputs.directive = 'all'
reconall.inputs.subjects_dir = self.FS_SUBJECTS_DIR
reconall.inputs.openmp = self.n_jobs
reconall.inputs.flags = "-3T"
reconall.run()
else:
print(
f"A freesurfer segmentation of subject {self.subject} already exists in {self.FS_SUBJECTS_DIR}"
)
from nipype.interfaces.freesurfer import ReconAll
import os
import shutil
import sys
##################################################
FREESURFER_HOME = os.environ.get('FREESURFER_HOME')
reconall = ReconAll()
# path to the subject T1 MRI image in .nii format
# this file must be in .nii format
nii_file_path = 'nii_file_path'
# Subject ID: this should be a string which defines the folder name
# that will be created automatically for the subject in /usr/local/freesurfer/subjects/
subject_id = 'subject_id'
print('Data preprocessing started for {subject} in {path}'.format(
subject=subject_id, path=nii_file_path))
reconall.inputs.subject_id = subject_id
reconall.inputs.directive = 'all'
reconall.inputs.subjects_dir = FREESURFER_HOME + '/subjects'
reconall.inputs.T1_files = nii_file_path
reconall.run()