Freesurfer November 2023

freesurfer@nmr.mgh.harvard.edu

69 participants
117 discussions

2 PhD positions in Prenatal programming of neurodevelopment in childhood
by Klara Mareckova 20 Nov '23

20 Nov '23

External Email - Use Caution Hello, I'm offering two PhD positions at the Faculty of Medicine, Masaryk University, Czech Republic, to study Prenatal programming of neurodevelopment in childhood. See more information at the links below and email me your CV at klara.mareckova(a)gmail.com if interested! :) Thanks, Klara Mareckova https://secure-web.cisco.com/1Md08Dmcg7DmgC-QMZFtqmVaw1faa3Fbv26fmwvBE4aZUH… https://secure-web.cisco.com/104yy20ksfCRxwDE7lc4YW3rRpd9GuI26hH_Oh8M5yBhov…

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Re: [Freesurfer] license issue with the updated version
by fsbuild 19 Nov '23

19 Nov '23

External Email - Use Caution  Please let us know if you are running MacOS 14 (Sonoma) on an Intel or silicon Mac (M1, M2 chip).    The system requirements at https://secure-web.cisco.com/10qwlQRot-nOOCuaXBtxsk1Ua4Tfh-PQlj0cP9-E6KzZM5… list MacOS 13 (Ventura) as the latest supported MacOS for the 7.4.1 release. - R. On Nov 18, 2023, at 18:29, Atena Akbari <atenaakbary(a)gmail.com> wrote:QObject::killTimer: Timers cannot be stopped from another thread

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license issue with the updated version
by Atena Akbari 18 Nov '23

18 Nov '23

External Email - Use Caution Dear freesurfer team I have uninstalled the previous versions of freesurfer on my mac (Sonoma 14.1), and have installed a new version 7.4.1 based on the step by step freesurfer installation info on the website. I have set the freesurfer home directory as follows: export FREESURFER_HOME=/Applications/freesurfer/7.4.1/ export SUBJECTS_DIR=path/to/my/data source $FREESURFER_HOME/SetUpFreeSurfer.sh and the license is in the /Applications/freesurfer/7.4.1. But when I run a freesurfer command I get the following error: ERROR: FreeSurfer license file /Applications/freesurfer/7.2.0/license.txt not found. QObject::killTimer: Timers cannot be stopped from another thread QObject::~QObject: Timers cannot be stopped from another thread /Applications/freesurfer/7.4.1//bin/freeview: line 2: 2938 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview "$@" Could you help me with this issue? thanks so much. Best, Atena

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Re: [Freesurfer] Unable to run recon-all
by fsbuild 17 Nov '23

17 Nov '23

External Email - Use Caution  The install location of freesurfer under /usr/local is on purpose read only (like the location of most Linux package installs) so you should not be trying to process and write subject data there.  We provide example subjects under /usr/local/freesurfer/7.4.0/subjects for read only purposes. Neither can you set SUBJECTS_DIR or write files in the process of running recon-all to your mounted or shared C drive.  This is because the the Windows file system does not support creating soft links. So please try the following.  In your Ubuntu linux terminal window,  go to your HOME directory and create a subjects directory there, i.e., you can always read/write to your HOME directory.   Then copy in your subject data to be processed there via recon-all and set SUBJECTS_DIR appropriately or pass the path on the recon-all command line. … in WSL linux terminal window …$ cd $HOME$ mkdir subjects$ cd subjects$ pwd/home/naily/subjects$ export SUBJECTS_DIR=/home/naily/subjects… copy in your data to process for recon-all to live under SUBJECTS_DIR … It also looks like your license file is not being found.  You can set the environment variable FS_LICENSE to point to that so it will be found and read, $ export FS_LICENSE=/home/naiy/license.txt$ head -1 $FS_LICENSEyou(a)somewhere.com       <---- email address you used to register … then try running some Freesurfer commands again … - R. On Nov 17, 2023, at 17:49, Nai, Ying Hwey <naiy@wustl..edu> wrote:<FSissues.txt>

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"error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast"
by Ludmila Midrigan 17 Nov '23

17 Nov '23

External Email - Use Caution Hi dear FS experts, I am having issues with ( I am assuming) the design matrix for my GM analysis. I am getting the error: "error: MatrixReadTxT: could not scan value [1][1] ERROR: loading C Path_to_contrast" I am only interested in a difference for Group ONE - Group ZERO; I am trying to run a DOSS ( with three groups and 4 nuisance covariates) my contrast is : [1 1 1 -1 -1 -1 0 0 0 0]/3 I have standardized all variables. Attached is the FSGD.xlxs file ( that I did transform into a .fsgd file) Please let me know what I'm doing wrong. Thank you so much! *milly mc * *"Life is a foreign language; all mispronounce it." * *Christopher Morley*

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Unable to run recon-all
by Nai, Ying Hwey 17 Nov '23

17 Nov '23

External Email - Use Caution Dear Freesurfer personnel, I downloaded and installed the latest version successfully following the instructions on windows WSL. However, I could not run recon-all. I then installed an older version, but I still could not run the recon-all. Could you please kindly advise me on how to resolve this issue? Thank you. Regards, Ying Hwey ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Segmentation of hippocampal subfields and nuclei of the amygdala
by Joshua Ezequiel Pasaye 17 Nov '23

17 Nov '23

External Email - Use Caution Hello, I am working on project using Freesurfer’s “Segmentation of hippocampal subfields and nuclei of the amygdala” to segment the hippocampal subfields and compare it with a software called ASHS developed by the Penn Image Computing and Science Laboratory at UPenn. For the data we collect, we get a ADNI3 T2w SPC vNav.08 iso, ADNI3 Accelerated MPRAGE.01 iso (T1), and the ADNI3 HighRes Hippocampal sequence (T2w). We edit the ADNI3 T2w SPC and ADNI3 Accelerated MPRAGE T1 using freesurfer. My question is which T2w sequence should I use to run the command: segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 [SUBJECTS_DIR]. The ASHS software uses the ADNI3 HighRes Hippocampal sequence so to compare the two outputs, it would be ideal to also use the HighRes Hippocampal sequence. Please let me know if you need additional information. Thanks, Joshua E. Pasaye, B.S. (he/him/his) Clinical Research Coordinator | Imaging Core Mesulam Center for Cognitive Neurology and Alzheimer's Disease Northwestern University – Feinberg School of Medicine 300 E. Superior Street, Tarry 8-734, Chicago, IL 60611 (312) 503-5675 | joshua.pasaye(a)northwestern.edu<mailto:joshua.pasaye@northwestern.edu>

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Running autorecon2-wm after wm edits makes no difference in final surface
by Fernanda Hansen P. de Moraes 17 Nov '23

17 Nov '23

External Email - Use Caution Dear FreeSurfer experts, I have been trying to manually correct a wm volume to further fix the wm and pial surfaces, but when I ran recon-all -subjid SUBJxxx -autorecon2-wm -autorecon3 nothing happened to the surfaces. I found an unknown-args.txt file under scripts, and it seems the autorecon2-wm flag is not recognized. How can I create new surfaces and overcome this issue? Here attached is the complete recon-all log file from the beginning, including all steps attempted. I would be very glad if you could help me overcoming this error to include as much subjects as possible in my project. Best regards, Fernanda Hansen P. de Moraes fernandahmoraes(a)gmail.com<mailto:fernandahmoraes@gmail.com> Pesquisadora no Instituto de Física da UFRJ | metaBIO (IF-UFRJ) Doutora em Ciências Médicas | Instituto D'Or de Pesquisa e Ensino

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Hippocampal subfields segmentation
by yunus soleymani 17 Nov '23

17 Nov '23

External Email - Use Caution Hello Freesurfer users, I was wondering if there is any Freesurfer code available for performing hippocampal subfield segmentation on multiple subjects simultaneously in parallel. I already have the code for analyzing a single subject, but I'm interested in analyzing hundreds of subjects at once. Thank you very much. Best regards,Yunus

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Mapping input volume (fa.nii) to hippocampus segmentation volume
by Mirsol Choi 16 Nov '23

16 Nov '23

External Email - Use Caution Hello Freesurfers, I am trying to segment the hippocampus into its subfields and take the FA values from each subfield area. I am able to segment the hippocampus using the command (segmentHA_T1.sh) and I was also able to perform the dt-recon function on dwi data. I am trying to map the fa.nii file from dt-recon into the hippocampus subfield volume rh.hippoAmygLabels-T1.v22.HBT.mgz, however when I run the code that is provided by vol2subfield -help: vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v21.HBT.mgz --outreg outreg.lta or vol2subfield --i fa.nii.gz --reg reg.lta --sf rh.hippoAmygLabels-T1.v21.HBT.mgz --o fa.rh.hbt.mgz I am met with a message stating "set: Variable name must contain alphanumeric characters." How can I fix this "variable name must contain alphanumeric characters" issue and run this command? Thank you all for your time, help and expertise. M

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Freesurfer November 2023