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.

prep_afni_surf 0.1                                January 2018                                 PREP_AFNI_SURF(1)