You could also do it pretty easily in matlab or python

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Douglas N. Greve
Sent: Friday, June 12, 2020 10:44 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Splitting surface overlay into separate files

When you say "surface" do you mean a surface overlay or a surface with xyz and neighbor relations? Assuming you mean an overlay (eg, something in an mgh or mgz file), you can try fscalc. Or do you have 25 frames  in a single file and you want to split them into separate files? You might be able to convert the mgh/mgz file to nii and use FSL tools and then convert them back (sometimes works, sometimes not)

On 6/12/2020 10:24 AM, Mason Wells wrote:

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Hi Experts,

Apologies if this is a rather simple question. Is there a FreeSurfer equivalent of fslmaths? I have an atlas overlay that has 25 visual areas in a single .mgz file. I want to separate each atlas region into a different file, so that I end up with 25 surface atlas regions. Is there a command that could achieve this?

My next question is whether or not there is a Freesurface command that can be used to complete surface based correlations. For example, if I want to check for the overlap between two ROIs. I have been using fslcc to do this in the volume, but perhaps freesurfer has something similar to do this on the surface?  

Cheers,

Mason

Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff    CF24 4HQ UK Email: WellsMT1@cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage

Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd    CF24 4HQ  DU E-bost: WellsMT1@caerdydd.ac.uk Ffôn: 02920 879628

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