Thank you very much for  the replies.

I checked the wiki and tutorial and I have successfully registered fMRI on the T1 images; the results were reasonable after checking with tkregister2. However, the "mri_vol2surf" fails producing  "Segmentation fault",  I don't know how to resolve it. Here is how I ran the whole process:

export SUBJECTS_DIR=/home/kayhan/test/myproject/control001/tp1
cd   ${SUBJECTS_DIR}/NIFTI
bbregister --mov fMRI.nii.gz --bold --s FREESURFER --init-fsl --reg bbregister/fmri-TO-orig.dat  --fslmat bbregister/fmri-TO-orig.mat


FREESURFER is the place the freesurfer files are. I have checked the results of the bbregister and it was fine. Here is how I called "mri_vol2surf" :

~$  mri_vol2surf  --mov fMRI.nii.gz --regheader FREESURFER --reg bbregister/fmri-TO-orig.dat  --hemi  lh  --o timeCourse.mgz
srcvol = fMRI.nii.gz
srcreg = bbregister/fmri-TO-orig.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
INFO: changing type to float
Done loading volume
Computing registration from header.
  Using /home/kayhan/test/myproject/control001/tp1/FREESURFER/mri/orig.mgz as target reference.
Reading surface /home/kayhan/test/myproject/control001/tp1/FREESURFER/surf/lh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 0 0 0
using old
Done mapping volume to surface
Segmentation fault



I would be thankful if you can help.

Thanks,

On Sun, Apr 1, 2012 at 2:34 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:

Hi Kaveh

use bbregister to register your functional data to the surface, then mri_vol2surf to sample it from the volume onto the surface and you should be all set.

cheers
Bruce

On Sun, 1 Apr 2012, Kaveh Kohan wrote:

Hi FreeSurfer Users,


I am new to the Freesurfer, I have a question regarding mapping of the
resting state fMRI time courses on the cortex area. I apologise in case my
question is naive. please bear with me:

Is it possible to have time-courses sampled from cortex? I mean how can I
get corresponding time-course for each vertex on the cortex ? I know that
FreeSurfer can produce mask for cortex are but I would like to have
time-courses on the flattened (2D) map; ie assuming that cortex is
flattened, each pixel of the 2D flattened image which resides in the cortex
(I guess it corresponds to a vertex on the cortex manifold?) is time-series.

I have ran recon-all on the T1. All of those operation were done using a
third party packages that uses freesurfer namely CMTK (http://cmtk.org). I
do not exactly know how to use "bbregister" to register the parcellation on
the resting-state fMRI image?

I would be thankful if you can help.


Thanks

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