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
____________________________________________________________________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Bruce Fischl <fis...@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
>
>
>
>
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