Hello Carina,

There is a bug in the current implementation of the ConcatenateSubregionsResults.sh script. A patch is now available herehttps://surfer.nmr.mgh.harvard.edu/pub/dist/lcnpublic/dist/ConcatenateSubregionsResults_Patch/ and is in the dev branch of FS. The script was incorrectly searching for the files you specified in the subjects’ mri/ folders and is now searching under the stats/ folders.

The fix described by Antoine should also work for you, but you have incorrectly specified the names of the *.txt files. However, I would strongly recommend using the patched version, as this will be the behavior going forward for nightly dev builds and stable releases.

Best, Jackson

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Carina Obermüller carina.obermueller@live.at Date: Monday, May 27, 2024 at 5:15 PM To: COSSA ANTOINE IDRS antoine.cossa@servier.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu, Carina Obermüller carina.obermueller@live.at Subject: Re: [Freesurfer] Group Stats for hipposubfields, brainstem and amygdalar

External Email - Use Caution Dear Antoine,

Thank you so much again for your reply! I did as you said and it seems like the script is on my computer now, but I get this error:

Could not find hipposubfields.rh.T1.v22.txt, skipping subject.

For all files. The first few lines looked like this:

carinaobermuller@MBP-di-Carina raw_data_freesurfer_Dec2023 % ConcatenateSubregionsResults.sh -f amygdalar-nuclei.lh.T1.v22.txt -f amygdalar-nuclei.rh.T1.v22.txt -f brainstem.v13.txt -f hipposubfields.lh.T1.v22.txt -f hipposubfields.rh.T1.v22.txt -s $PWD

cmd: /Applications/freesurfer/7.4.1/bin/ConcatenateSubregionsResults.sh -f amygdalar-nuclei.lh.T1.v22.txt -f amygdalar-nuclei.rh.T1.v22.txt -f brainstem.v13.txt -f hipposubfields.lh.T1.v22.txt -f hipposubfields.rh.T1.v22.txt -s /Users/carinaobermuller/Documents/raw_data_freesurfer_Dec2023

Gathering results from:

/Users/carinaobermuller/Documents/raw_data_freesurfer_Dec2023

Looking at files:

amygdalar-nuclei.lh.T1.v22.txt amygdalar-nuclei.rh.T1.v22.txt brainstem.v13.txt hipposubfields.lh.T1.v22.txt hipposubfields.rh.T1.v22.txt

Outputting results to:

/Users/carinaobermuller/Documents/raw_data_freesurfer_Dec2023

Concatenating stats for file: amygdalar-nuclei.lh.T1.v22.txt

Will write results to: amygdalar-nuclei.lh.T1.v22_concat.txt

Working on subject: Raw_TP1

Could not find amygdalar-nuclei.lh.T1.v22.txt, skipping subject.

Working on subject: Raw_TP2

Could not find amygdalar-nuclei.lh.T1.v22.txt, skipping subject.

Working on subject: T1w_AoC1001_T1_reor

Could not find amygdalar-nuclei.lh.T1.v22.txt, skipping subject.

Working on subject: T1w_AoC1001_T2_reor

Could not find amygdalar-nuclei.lh.T1.v22.txt, skipping subject.

The files are in the “stats” folder of each subject folder. I am wondering if the script is calling the files from a different folder? Or am I doing something else wrong?

Best wishes

Carina

Il giorno 24 mag 2024, alle ore 11:54, COSSA ANTOINE IDRS antoine.cossa@servier.com ha scritto:

Dear Carina,

I got the same problem at first, I thought it was coming from my computer. To resolve this, I simply downloaded the missing script file from here:MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/ftp/dist/freesurfer/dev_binaries/centos7_...https://secure-web.cisco.com/1P3_VeR3p4seMFU_4h_YDuZEeXwHEzHxThUx__-6Wf-M_OFWQqKTmTvHp71RI2elBqtTkbha89oeZVXhcpZANP9sHGVb4WLtmqqln-VZmQSQISaL_4G5Amhxs9aGiGZfyiAAASILFpth0Y6PVjHHSjwhV7SaEdnqWlPw3TkaHpMix5_7nm22xxrGoiIOcPbeqdDGqWsiNzoof6XNs2o1ulTNsShK2sf-_zEXBxCN4rmiv-MsCFiKlPZlK_5zoaLyU4BMVGv8_fB1GcZ8-wuOUKC-T9oVMAVMVJHgh5xI1l8706QZpBmISLBzgCr6AZfmd/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fftp%2Fdist%2Ffreesurfer%2Fdev_binaries%2Fcentos7_x86_64%2FConcatenateSubregionsResults.sh, put it in the bin folder of FreeSurfer and rerun the source command (source $FREESURFER_HOME/SetUpFreeSurfer.sh). This should fix your issue.

Kind regards, Antoine

________________________________ De : Carina Obermüller <carina.obermueller@live.atmailto:carina.obermueller@live.at> Envoyé : jeudi 23 mai 2024 17:01 À : COSSA ANTOINE IDRS <antoine.cossa@servier.commailto:antoine.cossa@servier.com> Cc : Carina Obermüller <carina.obermueller@live.atmailto:carina.obermueller@live.at> Objet : Re: Group Stats for hipposubfields, brainstem and amygdalar

CAUTION: This email originated from outside the company. Dear Antoine,

Thank you so much for your quick reply 😊

I ran this command in the directory that contains the free surfer file structure of my data, but it showed me that the command doesn’t exist:

ConcatenateSubregionsResults.sh -f amygdalar-nuclei.lh.T1.v22.stats -f amygdalar-nuclei.rh.T1.v22.stats -f brainstem.v13.stats -f hipposubfields.lh.T1.v22.stats -f hipposubfields.rh.T1.v22.stats -s $PWD

Do you know where I am going wrong here?

Kind regards Carina

Il giorno 22 mag 2024, alle ore 16:36, COSSA ANTOINE IDRS antoine.cossa@servier.com ha scritto:

Dear Carina,

I think you can refer to this page : ConcatenateSubregionsResults - Free Surfer Wiki (harvard.edu)https://secure-web.cisco.com/1CUyxaHfBCZieKC2UZBS0ojCN-NyonuQwz4rUPZ-Bj_M__nleJXQPgM-nSXdMZkNaevLpxuOFAIq_8scORVF1KEaf7FjaSkVhRQuwuhfnLBtrML9DssM3NhvJ35gov-zGsIWetz2UBcjNnjRJiIKWBfCsaF54vnnfi0G8SjRJho3B2aX4i_tkP4d-hwf6mg4bZ2LxMyHgx959hae3zMQUCTRqZC0hE0SODR-6-ShwFb204ypnH2BEAKy_xHNP1hb_Uny-QI7C_c3GNZG21pAjBekJMpcFNAkMjjQ7ryi73qCsNHRCwGFVKsqniK1hdSZC/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FConcatenateSubregionsResults and use the ConcatenateSubregionsResults.sh command 😉

Kind regards, Antoine ________________________________ De : freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> de la part de Carina Obermüller <carina.obermueller@live.atmailto:carina.obermueller@live.at> Envoyé : mardi 21 mai 2024 13:45 À : freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Cc : Carina Obermüller <carina.obermueller@live.atmailto:carina.obermueller@live.at> Objet : [Freesurfer] Group Stats for hipposubfields, brainstem and amygdalar

CAUTION: This email originated from outside the company.

External Email - Use Caution

Dear Freesurfer team,

I am looking for a group stats command like the asegstats2table and aparcstats2table command for hipposubfields, brainstem and amygdalar, but I couldn’t find it in the archives. I remember it was mentioned in the recent Freesurfer course, but I can’t find it anymore. Could you help me out? Also more generally, is there an overview page of all the possible group stats commands?

Thank you so much in advance for your reply!

Sincerely,

Carina

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