Thanks Anastasia. I have some problem when I use mri_binarize.FSL list and guide advise me to use label2surf. There are a way to obtain specific labels in .label instead of .nii.gz?

Stefano ----Messaggio originale---- Da: ayendiki@nmr.mgh.harvard.edu Data: 25-set-2013 17.49 A: stdp82@virgilio.it Cc: freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Import FS data to FSL

1 - Yes. 2 - You can use mri_aparc2aseg to grow the cortical labels into the white matter (say, by 2mm). The file that it will produce will be a volume file, so then you just run mri_binarize to extract specific labels. Make sure you save them in nifti format for FSL.

On Wed, 25 Sep 2013, stdp82@virgilio.it wrote:

Hi list,

I have 2 questions, please.

1-The bedpostX that I have run for TRACULA could be used for PROBTRACKX (FSL)?

2-I'd like to export cortical masks from FS to FSL.

An option is mri_binarize but this way failed in probtrackx (fsl). FSL list have advised me that I should use label2surf command to convert label to surface files.

Where could find the .label (according to FreeSurferColorLUT.txt) to build mask of frontal, parietal, motor, sensor, temporal and occipital lobes?

Do you have other ways that you advise me?

Thanks,

Stefano

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