Re: [Freesurfer] ROI masks created in FreeSurfer used in FSL??

Frank, can you send the commands you used and the terminal output? doug

On 01/09/2014 04:35 AM, Frank Hsieh wrote:

Hi Gari, Thanks so much for the tips! @ Doug: I basically followed the instructions on this site http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/ to obtain my ROIs. Any thoughts?

Many thanks! Frank

On Thu, Jan 9, 2014 at 1:22 AM, Garikoitz Lerma-Usabiaga <garikoitz@gmail.com mailto:garikoitz@gmail.com> wrote:

Hi,
sorry to jump in, but maybe this solves your problem. What I've
been doing is:

1.- Convert the .mgz ROI in Freesurfer to .nii format in FSL:
mri_convert --in_type mgz --out_type nii --out_orientation RAS
roi.mgz roi.nii

2.- Open the new roi.nii in mricron: mricron nu.nii -o roi.nii.
Select it in the menu and just save it as *_mricron.nii again. (I
converted nu.mgz with the same procedure as above to check that
the roi was in place). This was the only way to make it visible in
fslview and work with the roi in fsl afterwards.


Hope this workaround works for you!
Gari


On Thu, Jan 9, 2014 at 12:53 AM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    what was your mri_label2vol command and terminal output?
    doug

    On 01/06/2014 02:35 AM, Frank Hsieh wrote:
    > Dear FreeSurfer Users,
    >
    > I ran recon -all on my structural image and created ROI
    masks (using
    > mri_label2vol) based on FreeSurfer's cortical parcellation.
    I'd like
    > to use these masks for further analysis with FSL. However,
    it seems
    > that the ROI masks generated with mri_label2vol have
    different header
    > information than that of the original structural image. As a
    result, I
    > was unable to carry out further analysis with FSL (e.g.,
    converting
    > these ROI masks into functional space with
    hires2example_func.mat). I
    > was wondering if there is a way to solve this issue.
    >
    > Many thanks in advance.
    > Frank
    >
    >
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The information in this e-mail is intended only for the person to
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-- Frank