On May 7, 2021, at 20:17, Wei Shao <wshao@research.baycrest.org> wrote:

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Hello, there

I just want to follow up on this question, is there any command that I can use to extract the T2 sub-volume from two different groups of subjects(AVP and BAY) of the hippocampus from Freesurfer?

Best,

Wei

On Mon, May 3, 2021 at 8:13 PM Wei Shao <wshao@research.baycrest.org> wrote:

Hi, Abdalla Z Mohamed

Thanks for your reply, but this is code is for T1 scan only according to the instruction, I want to extract the volume from the T2 (for segmentation based only on the additional scan )

Best,

Wei

On Mon, May 3, 2021 at 7:55 PM <bio.abdallah2012@gmail.com> wrote:

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Hi Wei,

You can directly extract the volumes from all subjects within your Freesurfer Analysis folder by using the following command

quantifyHAsubregions.sh hippoSf T1 result.txt

 

Best regards,

Abdalla Z Mohamed.

 

 

From: Wei Shao
Sent: Tuesday, 4 May 2021 5:22 AM
To: Freesurfer support list
Subject: [Freesurfer] Question about hippocampal sub-volume extraction

 

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Hello,Dear Freesurfer exports 

 

I have a question about the pipeline of hippocampal sub-volume extraction:

quantifyHAsubregions.sh hippoSf <T1>-<analysisID> <output_file> <OPTIONAL_SUBJECTS_DIR>

Let's say I have two different groups of analysisID such as sub-AVP???? and sub-BAY????

 

I can pass a wildcard to extract the data of T2 scan from all sub-BAY???? subjects by quantifyHAsubregions.sh hippoSf BAY*-T2 result.txt

 

But Is there any way that I can extract the sub-volume from all the two different group subjects at one time? Thanks.

 

Best,

Wei

 

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