Freesurfer

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30130 discussions

GLM Using 2 Surfaces - Thickness and Area
by Tejaswi D. Sudhakar 18 Apr '24

18 Apr '24

External Email - Use Caution Hello Freesurfer team, I am interested in doing one glm analysis using both the thickness and cortical surface area. My question is two-fold: First, is it possible to provide both the thickness and area files to mris_preproc and mri_surf2surf commands or is it only possible to run two separate glms (one for thickness and one for area)? Second, can we consider thickness and area as separate values or are they both correlated? In other words, how correlated are the thickness and area values? Thanks in advances, Tejaswi

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gunzip error in load_mgh.m when file path contains spaces
by Tyler Slouf 18 Apr '24

18 Apr '24

External Email - Use Caution Hello FreeSurfer Developers, I found what I believe to be a bug. Typically I can load mgz files into my Matlab program without any trouble. But if the path containing the mgz file has a space then I get an error. When I run this very short script in Matlab calling the MRIread function (/Applications/freesurfer/7.4.1/matlab/MRIread.m): filepath = char("/Users/user/Documents/folder space test/data/mri.mgz"); mri = MRIread(filepath); I get the following error: gunzip: can't stat: /Users/user/Documents/folder (/Users/user/Documents/folder.gz): No such file or directory gunzip: can't stat: space (space.gz): No such file or directory gunzip: can't stat: test/data/mri.mgz (test/data/mri.mgz.gz): No such file or directory ERROR: problem reading fname SWITCH expression must be a scalar or a character vector. Error in load_mgh (line 163) switch type Error in MRIread (line 90) [mri.vol, M, mr_parms, volsz] = load_mgh(fspec,[],[],headeronly); Error in test_load_mgz (line 2) mri = MRIread(filepath); I traced this down to the function load_mgh.m (/Applications/freesurfer/7.4.1/matlab/load_mgh.m) where a file path string (char array) is dynamically populated with randomly generated folder names to unzip into. It's about line 69 and looks like this: [status,msg] = unix(sprintf('gunzip -c %s > %s', fname, new_fname)); You may notice that potential spaces in the path names fname and new_fname are not escaped with single quotes. I edited the file to escape the parameterized strings like so: [status,msg] = unix(sprintf("gunzip -c '%s' > '%s'", fname, new_fname)); This solved the problem for me. Computer details: OS: MacOS Sonoma (latest) Chipset: Apple M1 (aarch64) Calling Program: Matlab R2023b Freesurfer: 7.4.1 Thank you for your time. Sincerely, Tyler Slouf

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Skin-Skull-Brain segmentation
by XIE Jing 18 Apr '24

18 Apr '24

External Email - Use Caution Hello all, We would like to use FreeSurfer to remodel the head, not only including the detailed brain structural information, but also considering skin and skull. I am wondering if the FreeSurfer is possible to split the skin, skull and brain surfaces at the same time? We tried the syntax "mri_make_bem_surfaces -all" , and the error notes were received as follows: nvertices=2562, nfaces=5120 mri_strip_skull: triangle file /home/customer/Desktop/headmodel/FREESURFER/freesurfer/lib/bem/ic4.tri read trishrink: File /home/customer/Desktop/headmodel/MRI/-all/mri/brain/COR-.info not found Best guess at inner_skull.tri is in inner_skull_tmp.tri What's your suggestions and comments on this question? We appreciate it very much! Thanks in advance! Jing ------------------------------- Jing XIE Associate Professor Mechatronical Engineering Beijing Institute of Technology Beijing 180001, PR China

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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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