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Dear Sir,

I was able to generate segmentations as cited in the module , I am able obtain segmentations for CA1 posterior Head and CA1 Posterior body , along with  CA1 head and CA1 body , what does non posterior parcellations of CA1 head and body indicates, can these be assumed as anterior regions ?, is there any way to obtain CA1 head and CA1 body etc for both left and right hemispheres , as per segmentation results i can only see [lr]h.hippoSfVolumes-T1.v2x.mgz files  . Not  (lr)h.CA1_head and body , how can i split these subfields from  [lr]h.hippoSfVolumes-T1.v2x.mgz  files.


Thanks
Vasudev


On Tue, Jul 3, 2018 at 11:49 AM, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk> wrote:

Yes!


Juan Eugenio Iglesias

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/


From: Dev vasu <vasudevamurthy.devulapally@gmail.com>
Sent: Tuesday, July 3, 2018 12:22:27 AM
To: Iglesias Gonzalez, Eugenio
Cc: freesurfer@nmr.mgh.harvard.edu

Subject: Re: Anterior / Posterior Partition in Hippocampus parcellation atlas
 
Dear Sir,

I have another query if i use "export WRITE_POSTERIORS=1", will it generate posterior CA1 and other substructures in the form as cited  posterior_side_<substructure>_<T1>_<analysisID>_v2x.mgz , 


Thanks
Vasudev

On Mon, Jul 2, 2018 at 8:30 PM, Dev vasu <vasudevamurthy.devulapally@gmail.com> wrote:
Dear Sir,

Thanks for your reply Yes,i have run 6.0, Can you send me the link for developmental version of freesurfer, also how can i obtain posterior regions of subfields like CA1,CA2,CA3,CA4, as the link suggests only CA1 head and CA1 body were segmented , i need posterior part of CA1 can i assume CA1 body as posterior region.


Thanks
Vasudev

On Mon, Jul 2, 2018 at 8:25 PM, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk> wrote:

Ah, now I understand.

To get the division in the wiki (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala), you need to run the development version of FreeSurfer. The version you ran (6.0, I presume), does not provide such subdivision.

In principle, you could use Garikoitz’s code to subdivide the segmentation, but his code is not part of FreeSurfer, so you would have to contact him for support. Alternatively, you can also download the development version of FreeSurfer, which will provide the segmentation that I mentioned earlier.

Kind regards,

/Eugenio

 

-- 

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

 

 

From: Dev vasu <vasudevamurthy.devulapally@gmail.com>
Date: Monday, 2 July 2018 at 19:22
To: "Iglesias Gonzalez, Eugenio" <e.iglesias@ucl.ac.uk>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>, "iglesias@nmr.mgh.harvard.edu" <iglesias@nmr.mgh.harvard.edu>
Subject: Re: Anterior / Posterior Partition in Hippocampus parcellation atlas

 

Dear sir,

 

In the following journal published by you ,procedure for longitudinal segmentation was highlighted (https://github.com/garikoitz/hippovol) , I have run the module described in wiki and i have obtained lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz and lh.hippoSfLabels-T1.v10.mgz files , i would like to know how i can split the labels CA1 head, CA1 body and CA1 tail from this file, since individual subfield label numbers for CA1 head and CA1 body are not defined ,also can i assure CA1 body as posterior region and CA1 head as anterior ?.

 

 

Thanks

Vasudev

 

On Mon, Jul 2, 2018 at 7:39 PM, Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk> wrote:

Dear Vasudev,

You can run the module described in that wiki page, and in the output file [lr]h.hippoAmygLabels-T1.v2x.mgz you will find segmentations for CA1 head, CA1 body, CA23 head, CA23 body, CA4 head, CA4 body, and hippocampal tail (note that we don’t parcellate the tail).

Cheers,

/Eugenio

 

-- 

Juan Eugenio Iglesias

ERC Senior Research Fellow

Centre for Medical Image Computing (CMIC)

University College London

http://www.jeiglesias.com

http://cmictig.cs.ucl.ac.uk/

 

 

From: Dev vasu <vasudevamurthy.devulapally@gmail.com>
Date: Monday, 2 July 2018 at 17:09
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>, "iglesias@nmr.mgh.harvard.edu" <iglesias@nmr.mgh.harvard.edu>
Subject: Anterior / Posterior Partition in Hippocampus parcellation atlas

 

        External Email - Use Caution        

Dear Sir,

 

 

I have reviewed your journal which detailed about hippocampus parcellation ( https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala ) of subfields ( HBT - Head/body/Tail) , could you please let me know how to partition the atlas along the lines of Anterior CA1,CA3,CA4  and posterior CA1,CA3,CA4.

 

 

Thanks

Vasdudev

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