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.