Hi Mageshwar

gcs is a surface-based format for cortical segmentation. And it wouldn't be a conversion as much as it would be a training. If you can sample your regions onto the surface in .annot format you can use mris_ca_train to build a new gcs that you can then apply with mris_ca_label

cheers Bruce

On Thu, 5 Apr 2018, Mageshwar Selvakumar wrote:

Dear Bruce,

We would like to use a probabilistic atlas built upon by us (with 170 regions) on top of the harvard oxford atlas and would like to use this extended atlas to perform segmentation and analysis on freesurfer. We have these 170 regions in 170 different nifti files. I would like to know if we could use these regions in .nii or .mgz format and convert it to gcs format.

Thank you for your help,

Kind regards Mageshwar Selvakumar, M.Sc Department of Pharmakologische Bildgebung und Bildanalyse Friedrich Alexander Universität Erlangen Nürnberg

Office: Fahrstr. 17, 91054 Erlangen Phone: + 49-9131-8522898

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From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Thursday, April 5, 2018 3:35 PM To: Freesurfer support list Subject: Re: [Freesurfer] query regarding creating an atlas from nifti volumes.   Hi Mageshwar

what kind of an atlas are you talking about? We have multiple atlases for different purposes.

cheers Bruce On Thu, 5 Apr 2018, Mageshwar Selvakumar wrote:

...

Dear All,

I am a newbie to freesurfer and I would like to use our in-house built probabilistic atlas(each region as a binary mask and available as nifti files). I would like to create an atlas out of it

and

...

use it for our analysis. On searching the previous mailing list I came across a discussion where

the

...

volume information was converted into surface information and can be converted to labels and annotations but I couldn't find much documentation on creating an atlas directly from the volume

or

...

surface information. It would be nice if someone can point me out if this is possible and some relevant information to continue on it.

Thank you,

Kind regards

Mageshwar Selvakumar, M.Sc

Department of Pharmakologische Bildgebung und Bildanalyse

Friedrich Alexander Universität Erlangen Nürnberg

Office: Fahrstr. 17, 91054 Erlangen

Phone: + 49-9131-8522898