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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.m...https://secure-web.cisco.com/1y0oaAj8_46msfz3eab9vNnk8YQrv2-9xR9bXASOV_MJuEJI-SX94x6XB4dfwOmXlLycIfbwSJ08R1F18YK2tO1OXunPGnufbnmRAtxbIjBnd-2tOyktbIni_LkmfAF22Ib1d_j64GtmJN6W6P_NdiBDwFb879ejMjkqB6cZ7uF3gUrQXShMEGx9wDuwJS8Qry9eKUHyevUsFmqp4DT-bXpMfJwv_IZuyEUJcQEhWF386-uWm7xb8H7eoR8a9gr3PVGKMBW0D15CMbkSyKhW9ADnPONXev_wkFLcn31pPJvAqGFMpTw2V_p-tOrstv0G2/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine atMailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.massge...https://secure-web.cisco.com/1v_G4tfViUO0PitHCYTcVmk39R_yzC2VvNdgp58dPel26G5klxTLxik5MvD-8mbY_YbGyn_DXaDpoYlJnhKRL5fWaq0bPPtD8gzJv55DtEyM3YsUC9-hJ_BcdPjegUOeLbVT2E7ChLPJhVzUBLYg6FrzSvFC0vSB8qJKXdOj_8ci9Vlsy8g_KZxWI2o2ibtvzDLi5Uy0aXhKZVmeHtKmazDt-F5GX1jRIp8XTc2JFJ244y7HhmGDLdA6wU7ORu3zNC4Ls4QKr1UP55OCGBFEKSriRZV9IYDwa5NqqLJin87PTv5QjJQ2sgIYCl-FWkjQt/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.massge...https://secure-web.cisco.com/1v_G4tfViUO0PitHCYTcVmk39R_yzC2VvNdgp58dPel26G5klxTLxik5MvD-8mbY_YbGyn_DXaDpoYlJnhKRL5fWaq0bPPtD8gzJv55DtEyM3YsUC9-hJ_BcdPjegUOeLbVT2E7ChLPJhVzUBLYg6FrzSvFC0vSB8qJKXdOj_8ci9Vlsy8g_KZxWI2o2ibtvzDLi5Uy0aXhKZVmeHtKmazDt-F5GX1jRIp8XTc2JFJ244y7HhmGDLdA6wU7ORu3zNC4Ls4QKr1UP55OCGBFEKSriRZV9IYDwa5NqqLJin87PTv5QjJQ2sgIYCl-FWkjQt/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.