Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30070 discussions

Freesurfer 8.0 without processing directives
by Ben Wagner 07 Mar '25

07 Mar '25

External Email - Use Caution Hello Freesurfer devs, I'm trying to test Freesurfer 8.0 but I am encountering an error importing the T1 image. In previous versions I'd use this command "recon-all -s SUBJECT -i T1.nii" to import the data and then run "recon-all -s SUBJECT -qcache -all" to process. Under 8.0, when I run the import command I'm getting the error below, but basically the orig.mgz file is never created. It has been hinted in the help the processing directive was required in the past, has it finally become so? Thank, Ben mri_synthstrip --threads 1 -i /endosome/archive/shared/fs8_trial/SUBJECT/mri/orig.mgz -o /endosome/archive/shared/fs8_trial/SUBJECT/mri/synthstrip.mgz Configuring model on the CPU Running SynthStrip model version 1 Traceback (most recent call last): File "/project/shared/ANSIR/software/freesurfer/8.0.0/python/scripts/mri_synthstrip", line 261, in <module> image = sf.load_volume(args.image) File "/project/shared/ANSIR/software/freesurfer/8.0.0/python/lib/python3.8/site-packages/surfa/io/framed.py", line 41, in load_volume return load_framed_array(filename=filename, atype=Volume, fmt=fmt) File "/project/shared/ANSIR/software/freesurfer/8.0.0/python/lib/python3.8/site-packages/surfa/io/framed.py", line 119, in load_framed_array check_file_readability(filename) File "/project/shared/ANSIR/software/freesurfer/8.0.0/python/lib/python3.8/site-packages/surfa/io/utils.py", line 24, in check_file_readability raise FileNotFoundError(f'{filename} is not a file') FileNotFoundError: /endosome/archive/shared/fs8_trial/SUBJECT/mri/orig.mgz is not a file @#@FSTIME 2025:03:05:12:07:38 mri_synthstrip N 6 e 3.49 S 1.10 U 2.26 P 96% M 244216 F 0 R 84830 W 0 c 133 w 8576 I 0 O 0 L 4.08 4.28 4.24 @#@FSLOADPOST 2025:03:05:12:07:41 mri_synthstrip N 6 3.83 4.22 4.23 Linux Nucleus173 3.10.0-1160.88.1.el7.x86_64 #1 SMP Sat Feb 18 13:27:00 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s SUBJECT exited with ERRORS at Wed Mar 5 12:07:41 CST 2025 For more details, see the log file /endosome/archive/shared/fs8_trial/SUBJECT/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1ToDWv36nchbVd9vy63S26kW5fcy6Fqjicd_-OqrsrdXkot… ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Re: [Freesurfer] illegal instruction - core dumped with samseg lesion
by fsbuild 07 Mar '25

07 Mar '25

External Email - Use Caution  It looks like you installed the Ubuntu 22 freesurfer 7.4.1 package, i..e., freesurfer_ubuntu20-7.4.1_amd64.deb. Please list what linux OS you are running, the amount of memory/RAM on your machine, what the processor is on your linux machine and whether or not you are running linux in a virtual machine, e.g., on windows.   The processor on your machine may not be able to run all the instructions. - R. On Mar 3, 2025, at 09:10, Paola Di Filippo <paola.difilippo(a)unifg.it> wrote:        External Email - Use Caution        Hi everyone,I am using freesurfer v. 7.4.1 on a VM and I am trying to run samseg for an MS patient with the following command, but I get the following error: illegal instruction - core dumped. -------- freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME   /usr/local/freesurfer/7.4.1 FSFAST_HOME       /usr/local/freesurfer/7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR      /usr/local/freesurfer/7.4.1/subjects MNI_DIR           /usr/local/freesurfer/7.4.1/mni paolasofia@Freesurfer-ub22:~$ run_samseg --input /home/paolasofia/DICOM.ANG.CHER.2.4.91/NIFTI/A.C.2.4.91.MRI.12.9.22.T1.nii /home/paolasofia/DICOM.ANG.CHER.2.4.91/NIFTI/A.C.2.4.91.MRI.12.9.22.FLAIR_reg.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/paolasofia/LESION.SEG/A.C.2.4.91.MRI.2..9.22.LESIONS/ Illegal instruction (core dumped) any ideas on how I could solve the problem? thanks in advance _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1xFxPc3FuAhZNdTJxoXsQYpKoPEGds9ZI8k6t9qNnkFdUi…

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Re: [Freesurfer] Need to re-download for SAMSEG
by fsbuild 06 Mar '25

06 Mar '25

External Email - Use Caution  It would help to know what OS you are running on.  Some users have experienced issues with running the default shell, now zsh, on the Silicon Macs with M1 … M4 processors.  If you are on a silicon mac, then I would try running bash shell, e.g., see below for setting up the freesurfer environment on MacOS after running the freesurfer 8.0.0 .pkg installer.   You could also change your default shell to bash. No matter what OS you are running on, don’t forget to change SUBJECTS_DIR to a directory you can write to before processing your own subject data.  You don’t have write permission to modify where freesurfer is installed and where SUBJECTS_DIR points to by default. - R. % bash The 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/1NDBetOHTkHPkMteD2_GKgTsbI3gNgJ8PTsSsy9e3qS8Zh… export FREESURFER_HOME=/Applications/freesurfer/8..0.0 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a --------Setting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME   /Applications/freesurfer/8.0.0FSFAST_HOME       /Applications/freesurfer/8.0.0/fsfastFSF_OUTPUT_FORMAT nii.gzSUBJECTS_DIR      /Applications/freesurfer/8.0.0/subjectsMNI_DIR           /Applications/freesurfer/8.0.0/mni $ mkdir -p $HOME/subjects$ export SUBJECTS_DIR=$HOME/subjects  <--- copy in your subject data to here On Mar 5, 2025, at 11:11, Sebastian Adolfo Rios Quintanilla <sebas.riosq99(a)gmail.com> wrote:        External Email - Use Caution        Hello FreeSurfer Developers, I try using SAMSEG for my subjects' data. I acquired 3 subjects in 3 different months and everytime I wanted to use samseg for brain segmentation I encountered  "zsh: command not found" and found myself in the need to re-do all the installation steps. At first, after going from subject 1 to subject 2 I thought It was a mistake I may have made in the installation. But now after around a month, trying to work on subject 3 I get the same error. I reach out to the dev team because I plan to scan more subjects in the coming months and having to reinstall everytime is not efficient and time consuming. Thank you very much for your time, help and support. -Sebastian RiosMSc. student at Polytechnique Montreal, MTL, CA_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh..harvard.edu https://secure-web.cisco.com/1NyLa77_UEWtBNlbB1RgpkAgEBy-TX0mp6BnMjWNcHDqNm…

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Freesurfer 8 - ValueError: no field of name pixdim
by Lubig, Andreas 06 Mar '25

06 Mar '25

External Email - Use Caution Dear freesurfer team, I just tried to run recon-all on my T1 weighted images with the new freesurfer 8 version, but unfortunately the analysis stops with an error (it worked without any error using freesurfer 7). I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? the following problem occurred with image /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz : Traceback (most recent call last): File "/bif/software/FREESURFER/freesurfer-8.0.0/python/scripts/mri_synthseg", line 324, in predict image, aff, h, im_res, shape, pad_idx, crop_idx = preprocess(path_image=path_images[i], File "/bif/software/FREESURFER/freesurfer-8.0.0/python/scripts/mri_synthseg", line 577, in preprocess im, _, aff, n_dims, n_channels, h, im_res = get_volume_info(path_image, True) File "/bif/software/FREESURFER/freesurfer-8.0.0/python/scripts/mri_synthseg", line 1527, in get_volume_info data_res = np.array(header['pixdim'][1:n_dims + 1]) File "/bif/software/FREESURFER/freesurfer-8.0.0/python/lib/python3.8/site-packages/nibabel/wrapstruct.py", line 310, in __getitem__ return self._structarr[item] ValueError: no field of name pixdim resuming program execution ERROR: some problems occured for the following inputs (see corresponding errors above): /bif/storage/storage1/projects/migban/bidsdata/derivatives/freesurfer_v8/sub-AH002_ses-01_T1w.nii/mri/orig.mgz @#@FSTIME 2025:03:05:15:19:44 mri_synthseg N 11 e 8.65 S 0.72 U 4.20 P 56% M 575560 F 0 R 117516 W 0 c 260 w 14864 I 0 O 96 L 1.98 0.98 0.55 @#@FSLOADPOST 2025:03:05:15:19:53 mri_synthseg N 11 1.99 1.02 0.57 Linux synapse6 3.10.0-1062.12.1.el7.x86_64 #1 SMP Tue Feb 4 23:02:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-AH002_ses-01_T1w.nii exited with ERRORS at Wed Mar 5 15:19:53 CET 2025 With the command "fslhd" I get the following for the file: pixdim0 1.000000 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 2.530000 pixdim5 0.000000 pixdim6 0.000000 pixdim7 0.000000 1) FreeSurfer version: 8.0.0 (freesurfer-linux-centos7_x86_64-8.0.0-20250203-0f2bd3a) 2) Platform: CentOS Linux release 7.7.1908 3) uname -a: Linux synapse6 3.10.0-1062.12.1.el7.x86_64 #1 SMP Tue Feb 4 23:02:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached Thank you in advance. Best regards, Andreas Lubig

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changes in mris_anatomical)stats
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 05 Mar '25

05 Mar '25

External Email - Use Caution Hi all, For FS7.1.1, the previous commands for extracting annot files for lobeStrict was: mris_anatomical_stats --s sub-001_1 --hemi rh --lobesStrict rh.lobesStrict Seems like this command doesn't work anymore at least in FS7.4.1. What is the currrent commnd? The help for mris_anatomical_stats does not describe. Thanks, Victor Zeng Beth Israel Deaconess Medical Center PI: Keshavan, Lizano, Bolo -- ---------------------------------------------------------------------- PLEASE NOTE: This message is intended for the use of the person to whom it is addressed. It may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the intended recipient, your use of this message for any purpose is strictly prohibited. If you have received this communication in error, please delete the message and notify the sender so that we may correct our records. See our web page at http://secure-web.cisco.com/1VncDh6wJUWkzQkNofsJFV0nhBXTRJDhMupPiXc0_QV89dT… for a full directory of Beth Israel Lahey Health sites, staff, services and career opportunities.

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Need to re-download for SAMSEG
by Sebastian Adolfo Rios Quintanilla 05 Mar '25

05 Mar '25

External Email - Use Caution Hello FreeSurfer Developers, I try using SAMSEG for my subjects' data. I acquired 3 subjects in 3 different months and everytime I wanted to use samseg for brain segmentation I encountered "zsh: command not found" and found myself in the need to re-do all the installation steps. At first, after going from subject 1 to subject 2 I thought It was a mistake I may have made in the installation. But now after around a month, trying to work on subject 3 I get the same error. I reach out to the dev team because I plan to scan more subjects in the coming months and having to reinstall everytime is not efficient and time consuming. Thank you very much for your time, help and support. -Sebastian Rios MSc. student at Polytechnique Montreal, MTL, CA

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"Re:" text in the Subject: is okay
by 叶贝宁 05 Mar '25

05 Mar '25

External Email - Use Caution confirm 8055d10f3553375c75c1fa2ec5094235bf27c2f5

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cortical thickness group analysis
by Maria Czarnecka 04 Mar '25

04 Mar '25

External Email - Use Caution Hello, I am trying to run a group analysis on cortical thickness (two groups, no covariates). I have been trying to follow the tutorial (FsTutorialGroupAnalysis) but I run into a problem with the mri_glmfit. My script looks like this: fspath="/dat/freesurfer" for hemi in lh rh; do echo $hemi cd $fspath mri_glmfit \ --y ${hemi}.norm_${hemi}_thickness.mgh \ --fsgd /dat2/maria/scripts/final/group.fsgd dods \ --C /dat2/maria/scripts/final/group.diff.mtx \ --surf fsaverage ${hemi} \ --cortex \ --glmdir ${hemi}.group.diff.glmdir done I think the function is searching for " --y ${hemi}.norm_${hemi}_thickness.mgh" in the main freesurfer directory instead of going into each participant's folder. What am I missing? The first error that i get is: " ... FSGD /dat2/maria/scripts/final/group.fsgd labelmask /dat/freesurfer/subjects/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.group.diff.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.group.diff.glmdir Loading y from /dat/freesurfer/lh.norm_lh_thickness.mgh *error: mghRead(/dat/freesurfer/lh.norm_lh_thickness.mgh, -1): could not open file ... done reading.ERROR: loading y /dat/freesurfer/lh.norm_lh_thickness.mgh* ..." Does it mean that something is wrong with my group.fsgd file? A sample of this file, just in case: " GroupDescriptorFile 1 Title ThickBlinds Class Class1 plus blue Class Class2 circle green Input sub-NW01W Class1 Input sub-NW02W Class1 ..." I will be grateful for your help. Best, Maria Czarnecka

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Using HCP-MMP1 (Glasser) atlas with freesurfer
by Blum, August 04 Mar '25

04 Mar '25

Hi there, I'm on a linux machine, and trying to use the HCP-MMP1 atlas. I tried adding the corresponding .annot file to a freesurfer folder on a /usr/local/freesurfer filepath. However, my computer stated that I don't have permission. Let me know what I can do and if there's any more information that you need! Thank you, August Blum Clinical Research Coordinator I Early Brain Development Initiative Division of Psychiatric Neuroimaging Massachusetts General Hospital 149 13th Street, Charlestown, MA, 02129

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News: subregion probabilistic atlases in MNI space available
by Iglesias Gonzalez, Juan E. 03 Mar '25

03 Mar '25

Hi everyone, People have asked me to do this multiple times, and I finally got down to it: I put the subregion atlases (hippocampal subfields, nuclei of the amygdala, brainstem subregions, thalamic nuclei) in MNI/ICBM152 space. Details here: https://surfer.nmr.mgh.harvard.edu/fswiki/SubfieldAtlasesICBMspace Cheers, /Eugenio -- Juan Eugenio Iglesias http://www.jeiglesias.com

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