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?<br><br>I am using Ubuntu 10.10, the version of &quot;mri_vol2surf&quot; is &quot;stable5&quot;. Please let me knoe if more information is required.   Thanks.<br>
<br>~$ mri_vol2surf  --mov fMRI.nii.gz  --reg bbregister/fmri-TO-orig.dat  --hemi  lh  --o ./timeCourse.mgz  <br>srcvol = fMRI.nii.gz<br>srcreg = bbregister/fmri-TO-orig.dat<br>srcregold = 0<br>srcwarp unspecified<br>surf = white<br>
hemi = lh<br>reshape = 0<br>interp = nearest<br>float2int = round<br>GetProjMax = 0<br>INFO: float2int code = 0<br>INFO: changing type to float<br>Done loading volume<br>Reading surface /home/kayhan/test/myproject/control001/tp1/FREESURFER/surf/lh.white<br>
Done reading source surface<br>Mapping Source Volume onto Source Subject Surface<br> 1 0 0 0<br>using old<br>Done mapping volume to surface<br><b>Segmentation fault</b><br>using old<div class="h5"><br>
      </div><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div bgcolor="#FFFFFF" text="#000000"><blockquote type="cite"><div><div><div class="h5">
On Sun, Apr 1, 2012 at 2:34 PM, Bruce Fischl <span>&lt;<a href="mailto:fischl@nmr.mgh.harvard.edu" target="_blank">fischl@nmr.mgh.harvard.edu</a>&gt;</span>
        wrote:<br>
        </div></div><blockquote><div><div class="h5">
          Hi Kaveh<br>
          <br>
          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.<br>
          <br>
          cheers<br>
          Bruce
          <div>
            <div><br>
              On Sun, 1 Apr 2012, Kaveh Kohan wrote:<br>
              <br>
              <blockquote>
                Hi FreeSurfer Users,<br>
                <br>
                <br>
                I am new to the Freesurfer, I have a question regarding
                mapping of the<br>
                resting state fMRI time courses on the cortex area. I
                apologise in case my<br>
                question is naive. please bear with me:<br>
                <br>
                Is it possible to have time-courses sampled from cortex?
                I mean how can I<br>
                get corresponding time-course for each vertex on the
                cortex ? I know that<br>
                FreeSurfer can produce mask for cortex are but I would
                like to have<br>
                time-courses on the flattened (2D) map; ie assuming that
                cortex is<br>
                flattened, each pixel of the 2D flattened image which
                resides in the cortex<br>
                (I guess it corresponds to a vertex on the cortex
                manifold?) is time-series.<br>
                <br>
                I have ran recon-all on the T1. All of those operation
                were done using a<br>
                third party packages that uses freesurfer namely CMTK (<a href="http://cmtk.org" target="_blank">http://cmtk.org</a>).
                I<br>
                do not exactly know how to use &quot;bbregister&quot; to register
                the parcellation on<br>
                the resting-state fMRI image?<br>
                <br>
                I would be thankful if you can help.<br>
                <br>
                <br>
                Thanks<br>
                <br>
                <br>
                <br>
                <br>
                <br>
              </blockquote>
              <br>
              <br>
            </div>
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