Dear Sir,

I know there are approaches in Freesurfer for hippocampus subfield segmentation , but Freesurfer analysis takes a lot of time to process the imaging data that i have , Currently i have more than 50 subjects .

Could you please send me the subfield atlas that you have implemented if you have some documentation concerning details and nomenclature of different hippocampus subfields, i would be really glad.


Thanks
VAsudev

On 3 February 2017 at 12:17, Christian Gaser <[log in to unmask]> wrote:

Dear Vasudev,

maybe I am wrong, but this hippocampal subfield atlas is defined only in 3D images and not surfaces. The figure on the website shows the extracted surface of the isolated hippocampi, but there exist no surface atlas for that as far as I know.

Anyway, if your are interested in analyzing hippocampal subfields this is possible in CAT12 but only for 3D and not surfaces. I have implemented the same subfield atlas but have merged some regions because for 1mm isotropic spatial resolution some subregions are simply too small to be reliable (the original atlas is 0.3mm^3).

Please also check the information about the cobra atlas in ../toolbox/cat12/templates_1.50mm/cobra.txt. These are the merged regions:
CA1/CA2/CA3/stratum radiatum/subiculum/stratum lacunosum/stratum moleculare
CA4/dentate gyrus

In order to enable ROI analysis for cobra atlas comment out the resp. line for the cobra atlas in the cat_defaults.m file. Please keep in mind that this atlas implementation is not yet validated and there exists more sophisticated approaches (e.g. Freesurfer).

Best,

Christian

Christian Gaser, Ph.D.
Professor of Computational Neuroscience/Neuroimaging
Biomagnetic Center
Structural Brain Mapping Group
Department of Neurology
Jena University Hospital
Am Klinikum 1, D-07747 Jena, Germany
Tel: ++49-3641-9325778 Fax: ++49-3641-9325772
e-mail: [log in to unmask]
http://www.neuro.uni-jena.de


On 3 Feb 2017, at 11:39, Dev vasu wrote:

Dear  Sir,

I have surface based segmentation of hippocampus sub fields http://cobralab.ca/atlases/Hippocampus-subfields/   and i would like to incorporate them in my SBM analysis using each sub field as ROI , Could you please let me know if its possible through CAT 12  ?

Thanks
Vasudev

On 3 February 2017 at 09:40, Christian Gaser <[log in to unmask]> wrote:
Dear Vasudev,

CAT12 is using two different surface atlases that are provided by Freesurfer:
Desikan-Killiany (DK40) Atlas (2006)
Destrieux (a2009) Atlas (2009)

Therefore no additional atlas options in CAT12 are available. Moreover, it would be not appropriate to use hippocampus regions of a surface based atlas because because medial temporal regions are difficult to trace in the medial view of a surface.

Best,

Christian

On Thu, 2 Feb 2017 18:59:16 +0100, Dev vasu <vasudevamurthy.devulapally@GMAIL.COM> wrote:

>Dear Sir,
>
>Are there any surface based Atlas with segmented Hippocampus region in CAT
>12 ? , I have some .asc ( ascii) files from Freesurfer , how i could
>possibly turn them into Surface based atlas for SBM analysis.
>
>
>Thanks
>Vasudev
>