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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 wshao@research.baycrest.org *Sent: *Tuesday, 4 May 2021 5:22 AM *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1ElFYk2W8crrhUek2tE-Mwm4-KKwBJnP7zRoOg--stEzWjk...

Hi Wei, I think the easiest is to run quantifyHAsubregions.sh twice and manually concatenate the 2 output text files. Cheers, /Eugenio

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

On May 7, 2021, at 20:17, Wei Shao <wshao@research.baycrest.orgmailto: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.orgmailto: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.commailto:bio.abdallah2012@gmail.com> wrote:

External Email - Use Caution

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 Shaomailto:wshao@research.baycrest.org Sent: Tuesday, 4 May 2021 5:22 AM To: Freesurfer support listmailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Question about hippocampal sub-volume extraction

External Email - Use Caution 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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