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Hi. Dear Eugenio

Thanks for your reply, could you be more specific? I have tried many times with this command but with the same problem happened.

For example, I use the one subject 

quantifyHAsubregions.sh hippoSf  T1-AVP6176  At_risk/volume

And the feedback

Gathering results from subjects in:
   /home/weishao/At_risk
Using the prefix name:
   hippoSf
Using the suffix name:
   T1-AVP6176
And writing them to:
   home/weishao/At_risk/volume

However, there is no result text file in the output directory. 

[weishao@gra-login1 ~]$ cd At_risk/volume/
[weishao@gra-login1 volume]$ ls -ltr
total 0

The attachment is the original script of quantifyHAsubregions.sh 

Best,
Wei

On Thu, Apr 22, 2021 at 3:21 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

Dear Wei,

The syntax of the command is:

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

 

 

 

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.com 

 

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wei Shao <wshao@research.baycrest.org>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, April 22, 2021 at 15:10
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Question about volume matrix in hippocampus

 

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Hi, Eugenio

 

Thanks for your kind reply. I have tried this command with a dataset and it wasn't function.

 

For example, Here is my script 

 

#!/bin/bash

module load freesurfer/7.1.0
source $EBROOTFREESURFER/FreeSurferEnv.sh
export SUBJECTS_DIR=/home/weishao/At_risk

quantifyHAsubregions.sh hippoSf sub-AVP8580 sub-AVP6176 sub-BAY10224 /home/weishao/At_risk

And there is the feedback 

 

Gathering results from subjects in:
   sub-BAY10224
Using the prefix name:
   hippoSf
Using the suffix name:
   sub-AVP8580
And writing them to:
   sub-AVP6176
/project/6019291/shared/software/2017/Core/freesurfer/7.1.0/bin/quantifyHAsubregions.sh: line 8: cd: sub-BAY10224: No such file or directory
failed to do cd sub-BAY10224

 

I also tried this with one subject, 

 

And I don't find the text file at /home/weishao/At_risk,  I also tried this with one subject, couldn't find the text file neither.

 

Would you mind tell me where I did wrong? Thanks

 

Best,

Wei

 

On Wed, Apr 21, 2021 at 5:26 PM Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ@mgh.harvard.edu> wrote:

Dear Wei,

All the volume measurements use the underlying probabilities with the maximum level of granularity.

Kind regards,

Eugenio

 

 

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://www.jeiglesias.com 

 

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Wei Shao <wshao@research.baycrest.org>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, April 21, 2021 at 17:20
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Question about volume matrix in hippocampus

 

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Hi, Freesurfer experts.

 

I have used  "quantifyHAsubregions.sh hippoSf" to gather the volume information from the hippocampus. A quick question about the volume matrix, would you tell me which label system  ("HBT" "FS60" or "CA") this code used to extract the volume information? or there is no difference? Thanks

 

Best,

Wei

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