Hi Rick
Thanks for your kind response!
I set the PATH thing also in bash shell as you recommanded! Many thanks!

Probably I should ask this issue from @SUMA_Make_Spec_FS to Freesurfer, but if there are any suggestions you can give I'd also happy about that!
The output of 'mri_convert --help' is
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bash-3.2$ mris_convert --help
Usage: mris_convert [options] <input file> <output file>

This program will convert MRI-surface data formats.

Valid options are:
-p input is a patch, not a full surface
-c <scalar file> input is scalar curv overlay file (must still
specify surface)
-f <scalar file> input is functional time-series or other
multi-frame data (must specify surface)
--annot <annot file> input is annotation or gifti label data
--parcstats <infile> infile is name of text file containing
label/val pairs, where label is an annot name
and val is a value associated with that label.
The output file will be a scalar file.
--da_num <num> if input is gifti, 'num' specifies which
data array to use
--label <infile> <label> infile is .label file
label is name of this label
--labelstats <outfile> outfile is name of gifti file
to which label stats will be written
-o origname read orig positions
-s scale scale vertex xyz by scale
-r rescale vertex xyz so total area is
same as group average
-t subject apply talairach xfm of subject to
vertex xyz
-n output is an ascii file where vertex data
is the surface normal vector
-v Writes out neighbors of a vertex in each row. The first
column is the vertex number, the 2nd col is the number of neighbors,
the remaining cols are the vertex numbers of the neighbors.
Note: there can be a different number of neighbors for each vertex.
-a Print only surface xyz to ascii file
--combinesurfs <infile> <in2file> <outfile>
--delete-cmds : delete command lines in surface
--userealras : set the useRealRAS flag in the surface file to 1
--vol-geom MRIVol : use MRIVol to set the volume geometry
--to-scanner : convert coordinates from native FS (tkr) coords to scanner coords
--to-tkr : convert coordinates from scanner coords to native FS (tkr) coords
--volume ?h.white ?h.pial ?h.volume : compute vertex-wise volume, no other args needed
Note: --cras_add and --cras_subtract are depricated. They are included for backwards compatability
Use --to-tkr and --to-scanner instead
--cras_add : shift center to scanner coordinate center (was --cras_correction, which still works)
--cras_subtract : shift center from scanner coordinate center (reverses --cras_add)

These file formats are supported:
ASCII: .asc
ICO: .ico, .tri
GEO: .geo
STL: .stl
VTK: .vtk
GIFTI: .gii
MGH surface-encoded 'volume': .mgh, .mgz
Freesurfer binary format assumed for all other extensions.

EXAMPLES:

Convert a surface file to ascii:
mris_convert lh.white lh.white.asc

Write vertex neighbors to ascii:
mris_convert -v lh.white lh.white.neighbors.asc

Convert a surface file to ascii (vertices are surface normals):
mris_convert -n lh.white lh.white.normals.asc

Apply talairach xfm to white surface, save as binary:
mris_convert -t bert lh.white lh.white.tal

Convert a scalar overlay file to ascii:
mris_convert -c lh.thickness lh.white lh.thickness.asc

Convert a .annot file to Gifti label file:
mris_convert --annot lh.aparc.annot lh.white lh.aparc.gii

Convert a Gifti label file to .annot:
mris_convert --annot lh.aparc.gii lh.white.gii lh.aparc.annot

Convert a Freesurfer .label file to Gifti label format:
mris_convert --label lh.V1.label V1 lh.white lh.V1.label.gii

Create a scalar overlay file where each parcellation region
contains a single value:
mris_convert --annot lh.aparc.annot --parcstats lh.parcstats.txt\
lh.white lh.parcstats

See also mri_surf2surf
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Thank you very much!
MS



Edited 1 time(s). Last edit at 09/05/2019 12:38AM by vd.mpark.