On Mon, Apr 2, 2012 at 5:29 PM, Kaveh Kohan <kaveh.kohan@gmail.com> wrote:

No it did not work, mri_vol2surf still produces the same error (see below). In the link below, I have shared the freesurfer results (in the FREESURFER folder) plus fmri image (in the NITFI folder). I am wondering if there is anything wrong with my installation of the mri_vol2surf (stable 5). The data is anonymized.

http://dl.dropbox.com/u/7895831/tp1.tar.gz

--------------------------------- OUTPUT of mri_vol2surf

~$ 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 2:45 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

The new registration looks much better. The value I look at is the first value in the mincost file. For your data, it's about .6. This value will be between 0 and 1.1. There's no way to determine what a proper cut off is, but in your previous reg, the value as .9 or so, so .6 is probably fine. Did mri_vol2surf work with the new registration?
doug

On 04/02/2012 05:05 PM, Kaveh Kohan wrote:

I re-ran the registration with FSL (initfsl option) and the results looks fine to me. I have attached the new log file. If the results look fine and it does not produce error, is there any way that I check that my registration failed? Is there any term that I should search for in the log file? Do you think that the whole problem could be because of the headers of the files?

The de-identified data are already unloaded here. It contains the freesurfer results (in the FREESURFER foder) and the fmri image in the NIFTI folder. I would be appreciate if you can tell how to fix the problem with mri_vol2surf

http://dl.dropbox.com/u/ 7895831/tp1.tar.gz

Thanks,

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

<mailto: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>

<mailto: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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