read_surf.m will do the trick, but be sure to use 1-based indices! And note that the timeCourse.mgz you read is almost certainly a surface overlay with 137654 vertices and 236 time points, so if you read the surface f.vol(1,j,1,:) would be the timecourse for the jth index returned by read_surf
cheers, Bruce
On Tue, 3 Apr 2012, Kaveh Kohan wrote:
I think I figure out the problem with "mri_vol2surf". It seems that there is a bug in the executable. I switched to the older version of freesurfer (from 5.1 to 5.0) and it just works! I am not sure how to check the results. In matlab I used:
f = MRIread('timeCourse.mgz'); size(f.vol)
1 137654 1 236
it should be OK, right? It seems that there are 137654 voxels. BTW, how can I read the graph structure of the vertex, ie x,y,z of each vertex, which neighbors of each vertex etc?
In case you want to know the spec. of the sytem:
~$ uname -a Linux pc71 2.6.35-32-generic #67-Ubuntu SMP Mon Mar 5 19:39:49 UTC 2012 x86_64 GNU/Linux
maybe the mri_vol2surf is not compatible with this machine?
about the tar file, I just downloaded, it no probelm:
~$ wget http://dl.dropbox.com/u/7895831/tp1.tar.gz . kayhan kayhan 336958635 2012-04-03 20:09 tp1.tar.gz ~$ tar xvzf tp1.tar.gz
If you still unable to download it let me know I will find another way to upload it.
Thanks,
On Tue, Apr 3, 2012 at 6:06 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote: Can you double check that tar file? I get an error when I try to untar it -rw-r----- 1 greve greve 96469167 Apr 3 18:58 tp1.tar.gz
On 04/03/2012 04:15 PM, Kaveh Kohan wrote: > Any thought on this? I am wondering there might be something wrong > with FSL registration. I don't know what bbregister uses for > registration but as far as I know "flirt" is unable to register > 4d-image (such as fmri ) to 3D; it only accepts 3d as input and > output. Is it possible to register freesurfer surface on the mean > activation of fmri (therefore both 3d) and then sample from the > surface on the fmri space? > > Any reply is very appreciated. > > On Mon, Apr 2, 2012 at 5:29 PM, Kaveh Kohan <kaveh.kohan@gmail.commailto: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 mailto: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 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 <mailto: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 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 <mailto: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> <mailto:fischl@nmr.mgh mailto:fischl@nmr.mgh. harvard.edu http://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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