pymvpa2-prep-afni-surf1

Overview

usage: pymvpa2-prep-afni-surf [-h] [-v] [-s SID] [-d SURFDIR] [-a ANATVOL]

[-e EPIVOL] [-x EXPVOL] [-E {yes,no}] -r REFDIR

[-p STEPS] [-l LD] [--overwrite] [--hemi {l,r,l+r}] [-S {yes,no}] [--aea_opts AEA_OPTS] [-I] [-A {yes,no}] [-f {gifti,ascii}] [-T] [-t]

Anatomical preprocessing to align FreeSurfer surfaces with AFNI data.

It provides functionality to:

- convert FreeSurfer surfaces to AFNI/SUMA format (using SUMA_Make_Spec_FS).

- resample surfaces to standard topology (using MapIcosahedron) at various resolutions.

- generate additional surfaces by averaging existing ones.

- coregistration of freesurfer output to AFNI/SUMA anatomical or functional volume (using align_epi_anat.py).

- run @AddEdge to visualize coregistration.

- merge left (lh) and right (rh) hemispheres into single files (mh).

- generate various views of left+right inflated surfaces.

- generate SUMA specification files, and see_suma* shell scripts.

This script assumes a processing pipeline with FreeSurfer for surface reconstruction, and AFNI/SUMA for coregistration and visualization. Specifically it is assumed that surfaces have been reconstructed using FreeSurfer's recon-all. More details can be found in the documentation available at http://surfing.sourceforge.net

If EPIs from multiple sessions are aligned, this script should use different directories for refdir for each session, otherwise naming conflicts may occur.

This function does not resample or transform any functional data. Instead, surfaces are transformed to be in alignment with ANATVOL or EPIVOL.

For typical usage it requires three arguments: (1) "-e epi_filename" or "-a anat_filename" (2) "-d freesurfer/directory/surf" (3) "-r outputdir"' (*) "-T" [if "epi_filename" / "anat_filename" is in template (MNI/Tal) space"

Notes:

- Please check alignment visually.

- Nifti (.nii or .nii.gz) files are supported, but AFNI may not be able to read the {S,Q}-form information properly. If functional data was preprocessed with a program other than AFNI, please check alignment visually with another program than AFNI, such as MRIcron.