---
name: "pymvpa2-prep-afni-surf"
section: "1"
platform: "linux"
package: "python-mvpa2"
version: "2.6.0-1"
release: "Debian 9 (Stretch)"
platforms: ["linux"]
url: "https://new.carta.tech/pymvpa2-prep-afni-surf"
---

# pymvpa2-prep-afni-surf(1)

preprocess FreeSurfer surfaces for AFNI/SUMA

## NAME

prep\_afni\_surf - preprocess FreeSurfer surfaces for AFNI/SUMA

## DESCRIPTION

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.

## COPYRIGHT

Copyright 2010-2012 Nikolaas N. Oosterhof \<nikolaas.oosterhof@unitn.it\>

### optional arguments:

- **-h**, **--help**

  show this help message and exit

- **-v**, **--version**

  show program's version number and exit

- **-s** SID, **--sid** SID

  subject id used in @SUMA\_Make\_Spec\_FS

- **-d** SURFDIR, **--surfdir** SURFDIR

  FreeSurfer surf/ directory

- **-a** ANATVOL, **--anatvol** ANATVOL

  Anatomical that is assumed to be in alignment with the EPI data of interest

- **-e** EPIVOL, **--epivol** EPIVOL

  EPI data of interest

- **-x** EXPVOL, **--expvol** EXPVOL

  Experimental volume to which SurfVol is aligned

- **-E** {yes,no}, **--isepi** {yes,no}

  Is the experimental volume an EPI (yes) or anatomical (no)

- **-r** REFDIR, **-o** REFDIR, **--refdir** REFDIR

  Output directory in which volumes and surfaces are in reference to ANATVOL or EPIVOL

- **-p** STEPS, **--steps** STEPS

  Processing steps separated by "+"-characters. "all" is the default and equivalent to "toafni+mapico+moresurfs +skullstrip+align+makespec+makespecboth+makesurfmasks"

- **-l** LD, **--ld** LD

  MapIcosahedron linear devisions, e.g. 80, or 16+96 (for both 16 or 96). The default is 4+8+16+32+64+128

- **--overwrite**

  Overwrite existing files

- **--hemi** {l,r,l+r}

  Hemispheres to process (\[l+r\])

- **-S** {yes,no}, **--expvol\_ss** {yes,no}

  Skull strip experimental volume (\[yes\],no)

- **--aea\_opts** AEA\_OPTS

  Options given to align\_epi\_anat (\[-cmass cmass+xyz **-big\_move\]**)

- **-I**, **--identity**

  Use identity transformation between SurfVol and anat/epivol (no alignment)

- **-A** {yes,no}, **--AddEdge** {yes,no}

  Run AddEdge on aligned volumes (\[yes\])

- **-f** {gifti,ascii}, **--surfformat** {gifti,ascii}

  Output format of surfaces: 'ascii' (default - for now) or 'gifti'

- **-T**, **--template**

  Indicate that the experimental volume (suppplied by '-e', '-a', or '-x') is in template space. This will add "-Allineate\_opts '-maxrot 10 **-maxshf** 10 **-maxscl** 1.5'" to **--aea\_opts**

- **-t**, **--notemplate**

  Indicate that the experimental volume (suppplied by '-e', '-a', or '-x') is not in template space.

This function is \*experimental\*; using the **--overwrite** option may remove and/or overwrite existing files.