mp2rage_recon-all

usage:

mp2rage_recon-all.py [-h] [--fs_dir FS_DIR] [--spm_dir SPM_DIR] [--gdc_coeff_file GDC_COEFF_FILE] inv2 uni

example:

mp2rage_recon-all.py --fs_dir freesurfer \
                     --spm_dir /data/pt_02389/Software/spm12/ \
                     --gdc_coeff_file coeff_SC72CD.grad \
                     sub-08_ses-1_inv-2_MP2RAGE.nii \
                     sub-08_ses-1_UNIT1.nii

requirements

own code:

• mp2rage_recon-all.py
• anatomy.py
• run_gdc.sh

external software:

• freesurfer 7.1
• spm
• cat12
• matlab
• gradient_unwarp.py (https://github.com/Washington-University/gradunwarp, optional)
• fsl (imcp, convertwarp, applywarp)
• python 3

python packages:

• nipype
• nibabel=3 (gradient_unwarp uses functionality deprecated as of version 4.0)
• numpy (gradient_unwarp.py installation has some additional dependencies)