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> 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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MGH-NMR Center
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