On Mon, Apr 2, 2012 at 4:12 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

It looks like your registration failed (though it completed without error). Did you check it with tkregister? I don't think that would explain the segfault, but it is worth tracking it down.
doug

On 4/2/12 2:54 PM, Kaveh Kohan wrote:
I have also attached the "fmri-TO-orig.dat.log" maybe that has some useful information about the previous step (bbregister) .

On Mon, Apr 2, 2012 at 2:48 PM, Kaveh Kohan <kaveh.kohan@gmail.com> wrote:

No, it does not; sorry for the confusion. I have attached a clean output below. I don't know what it means. May be there is something wrong with the format of the files. Do you need me to upload the freesurfer results and fMRI somewhere for you to inspect it?

------------ OUTPUT

~$ mri_vol2surf --mov fMRI.nii.gz --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
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
------------

On Mon, Apr 2, 2012 at 1:44 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Hmmm, I don't know why it is doing that. Does it really print "using old" after the seg fault was that accidentally pasted in? It should not be printing that twice, maybe it's a clue.
doug

On 04/02/2012 10:26 AM, Kaveh Kohan wrote:

I have tried and it did not work (the same seg fault, see below). It seems that it successfully performs the mapping but it fails in final step probably saving the results. Is the data format that I used OK?

I am using Ubuntu 10.10, the version of "mri_vol2surf" is "stable5". Please let me knoe if more information is required. Thanks.

~$ mri_vol2surf --mov fMRI.nii.gz --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
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*
using old

On Sun, Apr 1, 2012 at 2:34 PM, Bruce Fischl

<fischl@nmr.mgh.harvard.edu <mailto: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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