Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

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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Re: [Freesurfer] NextBrain: no segment_fast or segment_fireants.py
by fsbuild 20 Jan '25

20 Jan '25

External Email - Use Caution   FS_HOME/python/packages/ERC_bayesian_segmentation/scripts/segment_fast.py isn’t in the 7.4.1 release from June of 2023 (now 2 years old).  You would need to switch to an install of one of the more recent packages from one of the development builds which you can find under, https://secure-web.cisco.com/1C2Ar2D42F31zW_7LdVanyLS5o5uQzqY0lbs-9lUFxdV56… There are some caveats that go along with switching to a different release, Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). - R. On Jan 20, 2025, at 05:54, AmirHussein Abdolalizadeh <amirhussein.a(a)gmail.com> wrote:        External Email - Use Caution        Hi Freesurfer users/experts, I was trying to run NextBrain (cloned from here: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/14eLrRV3Lqib6Tav7bYz9kPh7vG-KbczSql2Ct…) 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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1CDVwd9EaNYDWvqQc8hMimAN9CIoe95--mDhbMVqe2jheP…

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Re: [Freesurfer] Freesurfer remotely processing
by fsbuild 20 Jan '25

20 Jan '25

External Email - Use Caution  The freesurfer mri* commands can be run from a terminal window remotely via ssh’ing into a machine that has access to a local installation of freesurfer.  Hopefully your network connection is robust enough to keep up with your typing in the terminal shell window, and can display continuous output from the freesurfer commands you run. An X-windows server needs to be available on the machine where freeview runs in order to display the brain graphic images.   If you are going to run freeview on a remote machine, then X-Windows forwarding along with (hopefully some accelerated) Open GL graphics rendering is often setup so the images can be rendered there and then forwarded over the network to your machine.  That is faster/more efficient then trying to push more of the graphics over the network to be rendered with your local machines graphics hardware.  NoMachine, TightVNC, etc. could help with creating that connection. If you have an IT department, you should check with them to see if they already have specific machines setup for you to remotely login to - including forwarding images from X-Windows apps (like freeview) over the network to your machine. - R. On Jan 20, 2025, at 09:57, Fischl, Bruce R.,PHD <BFISCHL(a)mgh.harvard.edu> wrote:Hi Gonzalo Can you clarify what you mean? People use ssh all the time to log into remote machines and run recon-all (and freeview) CheersBruce From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Gonzalo Rojas Costa Sent: Monday, January 20, 2025 7:12 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer remotely processing         External Email - Use Caution        Hi:Is there any free implementation that allows me to process images with freesurfer remotely?Sincerely Gonzalo Rojas CostaMedicine SchoolFinis Terrae University_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer remotely processing
by Gonzalo Rojas Costa 20 Jan '25

20 Jan '25

External Email - Use Caution Hi: Is there any free implementation that allows me to process images with freesurfer remotely? Sincerely Gonzalo Rojas Costa Medicine School Finis Terrae University

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consensus on mp2rage or other t1w mri at 7T
by Jiaen Liu 17 Jan '25

17 Jan '25

External Email - Use Caution Dear community I'm wondering if there is a good consensus paper or other resources that can summarize the best practices of using high resolution T1w MRI at 7T and Freesurfer? We have a lot of mp2rage data which has nice uniformity but is affected by the background/skull noise. We use the second inversion time image INV2 to extract a brain mask to mitigate the issue. I'm not sure that's the best way. There are also tools like the robust mp2rage combination or the mprageise to remove the noise. We haven't systematically tested them yet. I'm wondering if these have been done and we can learn from previous experience. Thanks! Best regards, Jiaen Liu Ph.D. Assistant Professor Advanced Imaging Research Center & Radiology UT Southwestern Medical Center 2201 Inwood Ln Dallas, TX, USA, 75390 Office: 214.645.2750 Website: Liu (Jiaen) Lab | UT Southwestern, Dallas, Texas<https://secure-web.cisco.com/1k3jFgucLlYfBOkzupHE_iJP9vYs_l28g57vFBZ0AYA2d3…> ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Freesurfer