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Dear Vasudev, <begin copy from my last mail> 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. < end copy from my last mail> The cobra atlas is provided with CAT12. Please also read the html-help about this topic. Best, Christian On 3 Feb 2017, at 13:04, Dev vasu wrote: > 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 <+49%203641%209325778> Fax: ++49-3641-9325772 >> <+49%203641%209325772> >> 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 < >>> [log in to unmask]> 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 >>>> >>> >>> >>> >>