Re: [Freesurfer] How to flatten time course on the cortex

You should not use --regheader with --reg, but that should not have caused a seg fault. I'm not sure what went wrong, but try removing --regheader and see if it works. doug

On 4/2/12 2:38 AM, Kaveh Kohan wrote:

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 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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