""" running freesurfer reconall to get tissue segmentations from T1 subject_id = sd51_d01 data_dir = /data/pt_mar006/subjects free_dir = /data/pt_mar006/freesurfer Usage: $ python 02_structReconAll.py <subject_id> <data_dir> <free_dir> """ from nipype.interfaces.freesurfer.preprocess import ReconAll import os, glob, sys # subject_id and T1 scan directory: user given subject_id = sys.argv[1] data_dir = sys.argv[2] free_dir = sys.argv[3] Tscan = os.path.join(data_dir, subject_id, 'nifti/mprage', 'T1.nii.gz') # run ReconAll recon_all = ReconAll() recon_all.inputs.subject_id = subject_id recon_all.inputs.subjects_dir = free_dir recon_all.inputs.T1_files = Tscan recon_all.run()
""" running freesurfer reconall to get tissue segmentations from T1 subject_id = sd51_d01 data_dir = /data/pt_mar006/subjects free_dir = /data/pt_mar006/freesurfer Usage: $ python 02_structReconAll.py <subject_id> <data_dir> <free_dir> """ from nipype.interfaces.freesurfer.preprocess import ReconAll import os, glob, sys # subject_id and T1 scan directory: user given subject_id = sys.argv[1] data_dir = sys.argv[2] free_dir = sys.argv[3] Tscan = os.path.join(data_dir, subject_id, 'nifti/mprage', 'T1.nii.gz') # run ReconAll recon_all = ReconAll() recon_all.inputs.subject_id = subject_id recon_all.inputs.subjects_dir = free_dir recon_all.inputs.T1_files = Tscan recon_all.run()
