Freesurfer

freesurfer@nmr.mgh.harvard.edu

7 participants
30057 discussions

surface-based filtering
by Jiaen Liu 18 Apr '24

18 Apr '24

External Email - Use Caution I'm wondering if freesurfer provides functions to filter the surface data within certain neighborhood exclusively on the surface. It's essentially similar to regular smoothing in 3D space. But the filtering kernel only runs on the surface. I can think of a solution to filter adjacent vertex in the surface file. But I'm not sure if the adjacent vertex is also close in space. 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/1wkcO1DGr29TJIFWSpji3illMnzDHZyRdRD7_obcKaq5oL…> ________________________________ UT Southwestern Medical Center The future of medicine, today.

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BBRegistration with FSL topup
by Gianluca Guglietti 18 Apr '24

18 Apr '24

External Email - Use Caution Hi, I had a question as to how to integrate fsl's topup command for correcting B0 distortion with freesurfer's boundary-based registration. I am working with high-resolution epi data (0.8mm isotropic) with a reduced FOV and am trying to register it to an MP2RAGE structural scan that I've already run through free surfer's recon-all. When I use the BBR command it works perfectly fine but when I try to add the topup field map it fails, returning this error "MRIvol2surfVSM: vsm dimension mismatch 1". the field map was generated using two reverse phase encoded SE-EPI volumes with the same resolution and field of view as the GE-EPI BOLD data I am trying to register. Any advice would be greatly appreciated! Best, Gianluca

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question about infantfreesurfer
by Knut J Bjuland 18 Apr '24

18 Apr '24

External Email - Use Caution Dear freesufer experts, Does anyone know whether infantFreesurfer is ready to use for publication purposes? Thank you! Knut Jørgen Bjuland, PhD Telemark Hospital

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Default intensity values for gray and white matter
by Lokhandwala, Sanna 18 Apr '24

18 Apr '24

External Email - Use Caution Dear FreeSurfer developers, I am interested in understanding where the freesurfer default intensity values for gray and white matter specifically come from within the recon-all command. I understand the default intensity of white matter (mean) is 110, white matter (low) is 90, white matter (high) is 125, gray matter (low) is 30, and gray matter (high) is 100. I know that the default parameters are meant to improve segmentation of the gray and white matter tissue but could you please tell me how/where these values come from? I’ve read the 2002 paper “Whole Brain Segmentation: Automated Labeling of Neuroanatomical Structures in the Human Brain” and I saw that Figure 1 had varying distributions for gray and white matter intensity, but I did not see anything that explicitly stated how these default values were chosen. Your guidance is appreciated, Sanna Lokhandwala

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vertices are -1 when using vol2label
by Sam W 18 Apr '24

18 Apr '24

External Email - Use Caution Hello! I'm trying to convert the cerebellum cortex in the aparc+aseg.mgz into a label so I tried: mri_vol2label --c bert/mri/aparc+aseg.mgz --id 8 --l lh.cerebellum.label but the resulting output file only has -1 as vertices. Is there anything wrong with the command above? Best regards, Sam

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MRInormFindControlPoints
by Shahar Ben Noun 17 Apr '24

17 Apr '24

External Email - Use Caution Dear freesurfer team, I am attempting to use freesurfer using fmriprep but I get the following error message: error: No such file or directory error: MRInormFindControlPoints: could not find enough control points error: No such file or directory error: MRInormFindControlPoints failed I've searched the archive but couldn't find a solution. Does anyone have any thoughts on how to trouble-shoot this one? Also, I've attached the recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 2) Platform: Linux 3) PlatformVersion: 5.4.0-159-generic #176-Ubuntu SMP Mon Aug 14 12:04:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux Tue Apr 16 13:13:35 IDT 2024 4) recon-all.log: see attached Best regards, Shahar

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Re: [Freesurfer] Freeview problems
by fsbuild 17 Apr '24

17 Apr '24

External Email - Use Caution  You can check the post (quoted below) to verify the setup for the 7.4..1 release.   Instead of running the freeview command as listed in the post, you can run the mri_info command with no arguments to get the help info about the command line options.  If mri_diff runs and prints out the help output, then the issue is likely your command line arguments. - R.. bash-3.2$ mri_info USAGE: mri_info fname1 <fname2> <options>     --conformed : print whether a volume is conformed stdout    --conformed-to-min : print whether a volume is conformed-to-min stdout   <rest of output deleted> SETUP ENVIRONMENT https://secure-web.cisco.com/1-xQ9e5Z3VTlXilKkcSpNfmxzfXMzCk-PG0p40zknkFsd-… If you setup the Freesurfer environment ... here using bash and not zsh ... hostname ~ bash $ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ 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 .... and point FS_LICENSE to your license.txt file, e.g., in your $HOME directory .... $ cd$ pwd/Users/myuserid$ ls license.txtlicense.txt$ export FS_LICENSE=license.txt$ head -1 license.txtyou(a)somewhere.com  <---- email you used to register .... then try running from the command line  ... $ freeview $SUBJECTS_DIR/bert/mri/T1.mgz Please keep in mind you will need to change SUBJECTS_DIR to some other path, e.g., $HOME/subjects $ mkdir -p $HOME/subjects$ export SUBJECTS_DIR=$HOME/subjects .... and put files there if you want to write /modify subject files and data since /Applications/freesurfer/7.4.1/subjects is read only by default (not intended to be used to write data).

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Freeview problems
by Savoia, Alice (Stud. FPN) 17 Apr '24

17 Apr '24

External Email - Use Caution To whom it may concern, I am using freesurfer package on a MacBook Pro (macOS Sonoma, Version 14.1), but freeview shuts down immediately when I try to open any file. The license is in the correct place. Thank you for your help, Best regards.

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Error using mris_transform in Freesurfer 7.4.1
by Noemí Hostalet 16 Apr '24

16 Apr '24

External Email - Use Caution Hi, I'm trying to run the following mris_transform command in Freesurfer version 7.4.1: mris_transform group1/z/Freesurfer/surf/lh.smoothwm group1/z/Freesurfer/mri/transforms/talairach.xfm group1/z/Freesurfer/surf/tal/lh.smoothwm.tal.asc But it's giving the following error: The transform does not have the valid src volume info. Either you specify it with --trx-src or make the transform to have the valid src info. In a previous version (Freesurfer 5.3) it ran without problems. Do you know what could be the problem? Thank you -- Noemí

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Re: [Freesurfer] FreeSurfer Download and Install Error: Segmentation Fault
by fsbuild 15 Apr '24

15 Apr '24

External Email - Use Caution  If you setup the Freesurfer environment ... here using bash and not zsh ... hostname ~ bashThe default interactive shell is now zsh.To update your account to use zsh, please run `chsh -s /bin/zsh`.For more details, please visit https://secure-web.cisco.com/1RXVOTUqK1IY787C_o3ARLPP6BLZ_gJwBTdWVVnMp01gcO… $ export FREESURFER_HOME=/Applications/freesurfer/7.4.1$ 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 .... and point FS_LICENSE to your license.txt file, e.g., in your $HOME directory .... $ cd$ pwd/Users/myuserid$ ls license.txtlicense.txt$ export FS_LICENSE=license.txt$ head -1 license.txtyou(a)somewhere.com  <---- email you used to register .... then try running from the command line  ... $ freeview $SUBJECTS_DIR/bert/mri/T1.mgz Please keep in mind you will need to change SUBJECTS_DIR to some other path, e.g., $HOME/subjects $ mkdir -p $HOME/subjects$ export SUBJECTS_DIR=$HOME/subjects .... and put files there if you want to write /modify subject files and data since /Applications/freesurfer/7.4.1/subjects is read only by default (not intended to be used to write data). - R.On Apr 15, 2024, at 21:55, Angenelle Rosal <angenelle.rosal(a)mail.utoronto.ca> wrote:        External Email - Use Caution        Hello FreeSurfer Developers, I am currently using FreeSurfer 7.4.1 and I am attempting to upload the T1 image from subject “bert” using the terminal (I am using MacOS Ventura 13.5), as described in the demo video. However, freeview keeps quitting unexpectedly showing “2406 Segmentation fault: 11 $FREESURFER_HOME/Freeview.app/Contents/MAC0S/freeview “$@” when I type in “freeview/Applications/freesurfer/7.4.1/subjects/bert/mri/T1.mgz”. When I manually open Freeview without the terminal and load such image using the “Load Volume” tab, it works fine. I’ve searched the archives list and it might be due to the location of my license. However, I believe my license is located in the correct file, as it is located in my Freesurfer file (/Applications/freesurfer/license.txt). And so, any advice to also solve this problem would be greatly appreciated! Thanks     _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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