Freesurfer January 2025

freesurfer@nmr.mgh.harvard.edu

44 participants
67 discussions

aseg.mgz file not generated after recon-all
by Sara Rapuc 23 Jan '25

23 Jan '25

External Email - Use Caution Dear all, I ran FS recon-all -subcortseg -sd -subjid and it was completed without any errors. However, when looking into the mri folder, there is no aseg.mgz file, only aseg.auto.mgz. Could you please explain why this is and how to get the aseg.mgz file? Thank you. Best wishes, Sara

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Recon-all error...
by 박경일 23 Jan '25

23 Jan '25

External Email - Use Caution Dear FS Development Team, I recently encountered an error while running the recon-all process. This is the first time I’ve experienced an issue with this routine process. Please refer to the attached recon-all log file for detailed information regarding the error. Thank you for your time and support. Best regards, KI Park

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Re: [Freesurfer] FreeSurfer 8.0.0-beta: Stack smashing and normalization failures with 7T MP2RAGE data
by Michael Eyre 23 Jan '25

23 Jan '25

External Email - Use Caution Hi, thanks for your response, apologies for late reply. nu.mgz looks fine When I run tkregisterfv --s subject --fstal : orig.mgz(mov) is pretty well aligned to mni305.cor.mgz(targ) - images attached As you can see there is some signal dropout in the inferior temporal lobes but this is not unusual for 7T acquisitions, my other subjects have run without problems. thanks Mike Eyre ________________________________ From: Michael Eyre Sent: 11 January 2025 21:21 To: dgreve(a)mgh.harvard.edu <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] FreeSurfer 8.0.0-beta: Stack smashing and normalization failures with 7T MP2RAGE data Hi, thanks for your response, apologies for late reply. nu.mgz looks fine When I run tkregisterfv --s subject --fstal : orig.mgz(mov) is pretty well aligned to mni305.cor.mgz(targ) - images attached As you can see there is some signal dropout in the inferior temporal lobes but this is not unusual for 7T acquisitions, my other subjects have run without problems. thanks Mike Eyre

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Re: [Freesurfer] Freesurfer crashing (gui) or exting with error (command line)
by fsbuild 23 Jan '25

23 Jan '25

External Email - Use Caution  You don’t have permission to write to the default location of SUBJECTS_DIR as set in the freesurfer shell environment, i.e., /Applications/freesurfer/7.4.1/subjects.  The example subject data there is on purpose meant to be read only along with the rest of the freesurfer installation.  When it comes time to process your own subject data and write new or modify existing files, then you should set SUBJECTS_DIR to a path you always have write permission to, e.g., in your home directory,  $ mkdir -p $HOME/subjects$ export SUBJECTS_DIR=$HOME/subjects… place your data under $HOME/subjects and run your freesurfer/freeview commands .... - R. On Jan 23, 2025, at 06:00, Claas Philip Nähle <cp(a)naehle.net> wrote:        External Email - Use Caution        I am trying to create a 3D brain model from a *.nii file (here: test.niiI), which I have copied to the subjects folder. A) Using the command line, the following error messages appear: Phils-MacBook:~ cnaehle$ recon-all -s brain -all -i /Applications/freesurfer/7.4.1/subjects/test.niimkdir: /Applications/freesurfer/7.4.1/subjects/brain: Permission deniedfs-check-version --s brain --o /var/folders/xz/ydj4gf611v5gynjdql0mqzwr0000gn/T//tmp.8jh0SIERROR: cannot find brainrecon-all: version check failedfs-check-version --s brain --o /var/folders/xz/ydj4gf611v5gynjdql0mqzwr0000gn/T//tmp.8jh0SI Phils-MacBook:~ cnaehle$  With:Phils-MacBook:~ cnaehle$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1Phils-MacBook:~ cnaehle$ export SUBJECTS_DIR=$FREESURFER_HOME/subjectsPhils-MacBook:~ cnaehle$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/7.4.1FSFAST_HOME       /Applications/freesurfer/7.4.1/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/7.4.1/subjectsMNI_DIR           /Applications/freesurfer/7.4.1/mni Now, since this is for a 4th grade project for my daughter, it would be great if you could assist me. 1. Permssion denied: I have grant full disc access to Freesurfer and the terminal, but still….2. Error cannot find:  My Understanding is, that -s specifies the desired name of the output file, i. e. It will be created?3. Version check failed: No idea. B) Using the GUI, Freesurfer simply crashes. The crash log report is rather long as usual, but I can easily provide it if necessary. The Nifti file was created from DICOM images using Micron. Any advice would be greatly appreciated. Regards  Philip ------- Prof. Dr. Claas Philip Nähle cp(a)naehle.net +49-178-4001619 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1diz10loniHrO26jrUXhHQcZMRcpC86rmU8ogQ0yU3DutF…

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Freesurfer crashing (gui) or exting with error (command line)
by Claas Philip Nähle 23 Jan '25

23 Jan '25

External Email - Use Caution I am trying to create a 3D brain model from a *.nii file (here: test.niiI), which I have copied to the subjects folder. A) Using the command line, the following error messages appear: Phils-MacBook:~ cnaehle$ recon-all -s brain -all -i /Applications/freesurfer/7.4.1/subjects/test.nii mkdir: /Applications/freesurfer/7.4.1/subjects/brain: Permission denied fs-check-version --s brain --o /var/folders/xz/ydj4gf611v5gynjdql0mqzwr0000gn/T//tmp.8jh0SI ERROR: cannot find brain recon-all: version check failed fs-check-version --s brain --o /var/folders/xz/ydj4gf611v5gynjdql0mqzwr0000gn/T//tmp.8jh0SI Phils-MacBook:~ cnaehle$ With: Phils-MacBook:~ cnaehle$ export FREESURFER_HOME=/Applications/freesurfer/7.4.1 Phils-MacBook:~ cnaehle$ export SUBJECTS_DIR=$FREESURFER_HOME/subjects Phils-MacBook:~ cnaehle$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/7.4.1 FSFAST_HOME /Applications/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/7.4.1/subjects MNI_DIR /Applications/freesurfer/7.4.1/mni Now, since this is for a 4th grade project for my daughter, it would be great if you could assist me. 1. Permssion denied: I have grant full disc access to Freesurfer and the terminal, but still…. 2. Error cannot find: My Understanding is, that -s specifies the desired name of the output file, i. e. It will be created? 3. Version check failed: No idea. B) Using the GUI, Freesurfer simply crashes. The crash log report is rather long as usual, but I can easily provide it if necessary. The Nifti file was created from DICOM images using Micron. Any advice would be greatly appreciated. Regards Philip ------- Prof. Dr. Claas Philip Nähle cp(a)naehle.net +49-178-4001619

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Q: Tracula dmrirc file - set usethalnuc
by Kancsar Diana 22 Jan '25

22 Jan '25

External Email - Use Caution Dear All, I am encountering an issue while running Tracula from the dmrirc file. An additional line was required to run smoothly, without errors. I added " set usethalnuc = 0 " and it proceeded without errors, yet when " set usethalnuc = 1 " was added I encountered an error message. I might have missed some relevant information on the page, but could you please clarify what this setting does? Additionally, which preprocessing step might I have missed if Tracula only works with set usethalnuc = 0? Thank you for your help in advance! Kind regards, Diana PS: I am also enclosing the test dmrirc file that I was using.

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Re: [Freesurfer] SegmentAAN tool
by fsbuild 21 Jan '25

21 Jan '25

External Email - Use Caution  Thanks for sending along the log.  We will re-test SegmentAAN with the MCRV84 setup and follow up with you. - R. On Jan 21, 2025, at 11:19, Todd L Richards <toddr(a)uw.edu> wrote:        External Email - Use Caution        I am sending you the AAAN-nuclei.log file so you can see the error messages<AAAN-nuclei.log>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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NextBrain: no segment_fast or segment_fireants.py
by AmirHussein Abdolalizadeh 21 Jan '25

21 Jan '25

External Email - Use Caution Hi Freesurfer users/experts, I was trying to run NextBrain (cloned from here: https://secure-web.cisco.com/1UpUf_-L1H1hsaTNLobhBBGoHrKNtCqL7zDwyidsUOHZH8…) and asked HPC admin to install atlas_full and atlas_simplified in the designated folders, but encountered this error that segment_fast.py is not available in FS_HOME/python/packages/ERC_bayesian_segmentation/scripts/segment_fast.py (or segment_fireants.py). The code I run (in the folder of the downloaded tool): ./mri_histo_atlas_segment_fireants /path/to/input/T1.nii.gz /path/to/output/folder 0 dct I'm using FreeSurfer 7.4.1. Any help would be appreciated. Best, Amir

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SegmentAAN tool
by Todd L Richards 21 Jan '25

21 Jan '25

External Email - Use Caution I am sending you the AAAN-nuclei.log file so you can see the error messages

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SegmentAAN tool
by Todd L Richards 20 Jan '25

20 Jan '25

External Email - Use Caution I have followed your instructions and installed the 7-dev deb version of freesurfer from your link. But now this version of SegmentAAN wants to use MCRv97(which I did install using fs_install_mcr) which does not seem to have the right libraries for segmentNuclei so I also tried MCRv84 which is also missing libraries. Can you please send me the correct version of MCR that goes exactly with 7-dev version of SegmentAAN?

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Freesurfer January 2025