Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

aparc2aseg not working
by Jin Liu 09 Mar '25

09 Mar '25

External Email - Use Caution Hello FreeSurfer team, I’m trying to create a lobe segmentation for white matter. I first created the annotation files using mri_annotation2label with --lobesStrict for each hemisphere, and then tried to map the lobe parcellation onto segmentation volume by using mri_aparc2aseg. But somehow the resulting image was not segmented by lobes. It contains cortical parcellation by lobe, detailed subcortical segmentation by structure, and white matter is marked as a whole (cerebral white matter). I then checked the annotation files created by lobesStrict and they look fine, without any subcortical labels. I wonder where I made a mistake, or if there is an easier way to do lobe segmentation. The code I used is as follows: mri_annotation2label --subject 1300 --hemi lh --labelbase ./1300/label/aparc-lh --lobesStrict ./1300/label/lh.aparc.lobesStrict mri_annotation2label --subject 1300 --hemi rh --labelbase ./1300/label/aparc-rh --lobesStrict ./1300/label/rh.aparc.lobesStrict mri_aparc2aseg --s 1300 --annot aparc.lobesStrict --o ./1300/mri/lobesStrict.mgz Best, Jin

1 0

Re: [Freesurfer] illegal instruction - core dumped with samseg lesion
by fsbuild 09 Mar '25

09 Mar '25

External Email - Use Caution  If you can capture the first 100 or so lines of the core dump file, that could provide some additional information. I don’t see anything in the processor specs that excludes running AVX, SSE, etc. instructions, i.e., it is a recent Intel 14th generation processor, https://secure-web.cisco.com/16RohpBqIB1lAwZpTOwscE_gc2ArnH… being able to run those instructions would result in an illegal instruction error. As of August 2024, that 14th generation processor is also listed here,https://secure-web.cisco.com/1ZbvivIaAcYaPn-cIFZzBkR-9GU_4jH1NhKqB4nXL… perhaps it is crashing from the over voltage firmware bug, i.e., some postings indicate this will cause an illegal instruction error.  Intel has apparently issued a firmware update, but I don’t know how to verify if the processor has it.  Because a CPU could be damaged from over voltage, Intel extended the warranty for affected CPU’s when bought as individually boxed or when the CPU comes installed on a system motherboard as part of an out of the box machine.   You would have to contact the vendor you bought either the individual CPU or machine from to see if you qualify for a replacement.  But I would at least try to make sure the firmware is up to date for the CPU. I think you would see a different error if the VM was not allocated enough RAM or CPU cores, or if the process was running out of swap or disk space.   If you've seen crashes like this when running other perhaps compute intensive software, then that would also point to the firmware issue.. - R. On Mar 7, 2025, at 05:53, Paola Di Filippo <paola.difilippo(a)unifg.it> wrote:Intel(R) Core(TM) i5-14600K

2 1

Problems with Bayesian Segmentation with Histological Atlas "NextBrain"
by Lukas von Erdmannsdorff 09 Mar '25

09 Mar '25

External Email - Use Caution Dear Freesurfer Developers, First of all, thank you for the fantastic work on the Histo Atlas Segmentation tool and the amazing updates in FreeSurfer 8! Since I encountered some crashes with mri_histo_atlas_segment_fireants and mri_histo_atlas_segment_fast, I wanted to share the issues I experienced. I downloaded FreeSurfer 8 to my M1 MacBook Pro using the installation package, but it partially contains an older code version compared to the one on GitHub for the NextBrain segmentation with FireAnts. For example, it attempts to import FireAnts packages that are not included, such as GreedyRegistration from fireants.registration. I then installed FreeSurfer 8 directly from GitHub, which worked. However, as soon as EasyReg started, I encountered a thread lock. This also occurred when trying to run the EasyReg step directly as a terminal command. After that, I attempted the installation on Linux. However, in the latest installation package for Ubuntu 18, the ERC_bayesian_segmentation folder was completely missing. I then installed it again directly from GitHub but ran into a similar issue with EasyReg during the mri_histo_atlas_segment_fireants process, even when using only a single thread. I also tried mri_histo_atlas_segment_fast because my data is 1mm isotropic. However, this also did not work, as it failed when starting the registration with SynthMorph. I was able to resolve this by using the spawn method for multiprocessing, preventing issues when processing both hemispheres simultaneously. Additionally, I noticed that mri_TumorSynth is missing, although it is listed on the FreeSurfer wiki page. I hope it will be available in an updated version of FreeSurfer 8. Thanks in advance! Best regards, Lukas von Erdmannsdorff

1 0

Hypothalamic subunits segmentation: volumes = 0
by Miguel Ángel Rivas Fernández 07 Mar '25

07 Mar '25

External Email - Use Caution Dear FreeSurfer devs, I have tried to use the hypothalamic segmentation tool on my T1w data (voxel size = 1mm), but in in some subjects, one of the volume measurements of the structures is equal to 0. I have used the following command: mri_segment_hypothalamic_subunits --i /home/user1/data/scans/ --o /home/user1/data/segmentations/ --vol /home/user1/data/hypothalamic_volumes.csv I am using FreeSurfer version 8.0.0. Am I forgetting any important flag in the command? Any help to solve this issue would be appreciated. Thank you very much for your time. Best, -- *Miguel Ángel Rivas Fernández*

2 2

letter
by Fischl, Bruce R.,PHD 07 Mar '25

07 Mar '25

Hello FS List I'm sending the following letter: https://docs.google.com/document/d/1pie-bVZHm_iQneZrfkGKX8hiRXLuIJy6CvuXjcn… to the Boston Globe. Anyone in the US that wants to sign it is welcome to paste their signature in at the end. IMO if your immigration status is vulnerable you should *not* sign it. I'll keep it open as long as I can, including ideally after the letter itself is published, but we'll see how it goes. Thanks Bruce

3 3

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.

2 3

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…

2 1

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…

1 0

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

2 3

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.

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer