Freesurfer April 2025

freesurfer@nmr.mgh.harvard.edu

40 participants
53 discussions

longitudinal analysis on one subject
by Isabella Rossellini 13 Jul '25

13 Jul '25

External Email - Use Caution Hello Freesurfer users/experts, I am working with Freesurfer 7.4.1 on a MacStudio (macOS 15.2) and I would like to ask your opinion about the following. Basically, we had an anxiety treatment study and I would like to analyze one subject who has 5-time points (0, 3, 6, 9, 12) with a longitudinal pipeline, two-stage model. Is it possible to run this on one person only and see the changes between these time points? I have never done this before on one subject so I am not sure what the best approach would be to look at the changes. After running the longitudinal preprocessing (base, long), should I generate the tables of freesurfer parcellation/segmentation stats data (aparcstats2table, asegstats2table)? Or can I just follow the two stage model steps? Maybe glm only works on a group of subjects. https://secure-web.cisco.com/1iC7gpXrtEAUPrcmI22C302poe7thUhcUmsjgK95UydNOq… (We have 9 more subjects - 10 in total - so I was hoping to visualize the pattern of changes one by one, in each subject, since these patients showed different changes in anxiety based on self-reported questionnaires) Sincerely, Isa Rosselini

2 7

Updates/bug fixes available for the 8.0.0 release
by fsbuild 27 Jun '25

27 Jun '25

External Email - Use Caution Some updates/bug fixes are available for an existing installation of the Freesurfer 8.0.0 release.  The list of files you can update along with a brief comment about the change(s) are: $FREESURFER_HOME/bin/csvprintScript changed to use python3 - values for eTIV should no longer be misreported as 0.00 for data processed with the recon-all command $FREESURFER_HOME/bin/recon-allFixes for options -autorecon1, -nonuintensitycor.  Add flag -no-fix-ga to turn off fixing of gyrus ambiens part of the cortex label. $FREESURFER_HOME/bin/gtmseggtmseg now uses samseg by default $FREESURFERR_HOME/bin/xhemiregModifications to make xhemireg work with 8.0. $FREESURFER_HOME/bin/xcerebralseggtmseg now uses samseg by default $FREESURFER_HOME/bin/post-recon-allgtmseg now uses samseg by default $FREESURFER_HOME/python/packages/gems/SamsegLongitudinal.pyfix parameters to surfa.image.transform() $FREESURFER_HOME/etc/recon-config.yaml Added option -no-fix-ga to turn off fixing of gyrus ambiens part of the cortex label. Please note THESE UPDATES DO NOT CHANGE THE OUTPUT OF THE recon-all COMMAND. If these updates are of interest to you, then please go the 8.0.0 download URL,https://secure-web.cisco.com/15mh8yOb2RWi2iQyUfX1LgM0gB5PobUejtWnQDIeOm… and download the fs8_update.sh script. On MacOS run the script as follows,$ sudo FREESURFER_HOME=/Applications/freesurfer/8.0.0  bash  fs8_updates..sh On CentOS and Rocky8 Linux run the script as follows,$ sudo FREESURFER_HOME=/usr/local/freesurfer/8.0.0-1  bash  fs8_updates.sh On Ubuntu Linux run the scripts as follows,$ sudo FREESURFER_HOME=/usr/local/freesurfer/8.0.0  bash  fs8_updates.sh You will be prompted on the command line as to whether or not you want to install each file, including displaying the description of the change(s) listed above.

2 1

Re: [Freesurfer] Question on using thalseg_1.1.h5
by Georgios Argyropoulos 23 May '25

23 May '25

External Email - Use Caution Many thanks and apologies, Henry - I figured it out... I stupidly replaced your improved segmentation script in both the scripts and the bin directory instead of only replacing the former. many thanks for your time, much appreciated g

2 5

mri_cc segementation fault during recon-all using FreeSurfer 8.0.0
by 김근유(의과대학 정신과학교실) 06 May '25

06 May '25

External Email - Use Caution I'm attempting recon-all command with "-all -qcache" option with T1w nii.gz file. I got the following error in all of my subjects data. ------ freesurfer-macOS-darwin_arm64-8.0.0-20250205-0f2bd3a FreeSurferEnv.csh dev Darwin gimgeun-yuui-MacBookPro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:27:24 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T6000 arm64 ~/Dropbox/KKY/Imaging/FS_subjects/05731016/mri ~/Dropbox/KKY/Imaging/FS_subjects/05731016/mri IsConformed yes Mon Apr 14 18:40:16 KST 2025 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta transforms/cc_up.lta 05731016 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as transforms/cc_up.lta Segmentation fault ERROR: mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta transforms/cc_up.lta 05731016 Darwin gimgeun-yuui-MacBookPro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:27:24 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T6000 arm64 recon-all -s 05731016 exited with ERRORS at Mon Apr 14 18:40:17 KST 2025 To report a problem, see http://secure-web.cisco.com/1OIbiZUZzpMZLVXGKj-AwW4K8SnoS4EHxuX0Nm7vR74Z11F… ------ I've used Freesurfer version 7.4.1 without this error in my computer. "aseg.auto_noCCseg.mgz" was only 16 bytes. And when I inspected "synthseg.vol.csv" in "stats" folder, the volume of all segments was 0. [image: image.png] I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log in case it's of any use. 1) FreeSurfer version: MacOS X darwin_arm64 (64b) PKG installer (Silicon Macs with M1...M4 processors) -- with the latest version of Xquartz 2) Platform: macOS Somoma 14.1 3) uname -a: Darwin gimgeun-yuui-MacBookPro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:27:24 PDT 2023; root:xnu-10002.41.9~6/RELEASE_ARM64_T6000 arm64 4) recon-all.log: see attached Thank you for your cooperation. Best regards KY, Kim -- *Keun You, KIM (김근유), MD, PhD* Assistant Professor Department of Psychiatry (Geriatric Psychiatry) Severance Hospital Yonsei University College of Medicine Seoul, Republic of Korea

2 1

Fully-funded PhD studentship at UCL
by Holmes, Emma 06 May '25

06 May '25

External Email - Use Caution Dear all, I am currently advertising a fully-funded studentship at UCL, open to UK applicants. We'll develop training programmes that aim to help people with hearing loss to listen more easily in noisy environments. The project uses auditory psychophysics and pupillometry. Project: Auditory training interventions to improve speech understanding in noisy environments Supervisors: Emma Holmes & Stuart Rosen Location: UCL, London Funder: RNID The position is open to UK applicants. The application deadline has been extended to 7th May 2025. The full details and job description can be found at the following web page: https://secure-web.cisco.com/1TNEjB4pAbgNaMjkDqkEFrfZmZsz5_IFeOlNifuH77HKCa… (or downloaded directly from the following link: https://secure-web.cisco.com/1tbRn-Pi-qRxr1VWXUMEjd5_qTSHm4AmZERGkpjxWXlc60…) Potential applicants are welcome to get in touch with me (emma.holmes(a)ucl.ac.uk) for informal queries about the position, or to discuss the position further. Please share this with any students/colleagues in your networks who may be interested. Best wishes, Emma Emma Holmes Associate Professor in Speech and Hearing Science, UCL (she/her) e-mail: emma.holmes(a)ucl.ac.uk lab website: https://secure-web.cisco.com/1oy7PuZmYuDbJbMTcDdge6uriW-uez1cnDegPIJOXaw45L… personal website: https://secure-web.cisco.com/1SnWUfJYm3Tdui-okbpxsWhAocSIqrLHQf2nQJLfewHLC8… twitter/X: @Emma_Holmes_90<https://secure-web.cisco.com/1gXix978hov1V9SodYHxm5RTrkenNuXdAfn-9GpIW7Sjtz…> bluesky: @emmaholmes90.bsky.social<https://secure-web.cisco.com/1LnHqmcEvnKohjCDjZh_Yz1iHhKwm4rqW4kjx6qztckzld…> Mailing Address: Department of Speech Hearing and Phonetic Sciences Chandler House 2 Wakefield Street London WC1N 1PF United Kingdom Let me know if I can make any adjustments related to disability or neurodivergence to improve how we interact. Please note that I don't expect you to respond to emails outside of your normal working hours.

1 1

Longitudinal pipeline - failed single timepoint segmentation
by Dorian Pustina 01 May '25

01 May '25

External Email - Use Caution Hi all, I have some questions regarding failed segmentations on longitudinal data. We have large datasets of Huntington's disease with data collected longitudinally for 3-10 years. Freesurfer is our main tool to extract volumetric scores, particularly in caudate and putamen. I usually QC Freesurfer segmentations and include the fail/pass status for other researchers to use. I inspect the segmentation of the cross-sectional pipeline because I noticed that mis-segmentations are clearer and the longitudinal pipeline does not seem to correct them. For example, a displaced putamen segmentation in cross-sectional pipeline becomes just more fuzzy in the longitudinal pipeline with more peppered voxels at the edges. So basically, my QC of the cross-sectional segmentation decides if the timepoint is good or not. I have three questions: 1. Is my understanding correct that a motion corrupted scan (i.e., with motion rings) is going to affect the other timepoints by compromising the SST? Thus the only solution would be to exclude the motion corrupt timepoint from FS processing? And in case the timepoint has been processed with FS, is the best practice to exclude the entire subject given that the bad scan have compromised the accuracy of other timepoint segmentations? 2. On a different scneario, if a timepoint has a good scan but Freesurfer's segmentation is simply innacurate or displaced, is this bad segmentation at the cross-sectional level going to affect the other timepoints after running the longitudinal pipeline? 3. This is the most important question: is there a common recommendation or practice how to deal with failed segmentations in the longitudinal pipeline? Correcting manually the segmentations is not an option, so I am asking whether we can just exclude the failed segmentation timepoint from the analysis or whether we should exclude the entire subject? Thank you for sharing any thoughts. I cannot seem to find information on this topic on papers or the mailing list, so any tips on how you or your lab deals with these issues can help. Dorian

3 3

Inquiry about the gtmpvc --reg-identity flag
by Y Zeng 01 May '25

01 May '25

External Email - Use Caution Hi, I am currently using mri_gtmpvc from PETSURFER for partial volume correction. I have registered the PET image to nu.mgz to get the coregistered PET image (in 1mm T1 space). As I also want to get the final output after PVC in the same space as PET scans, I use the –reg-identity flag, and the coregistered PET scan rather than the original PET scan as input. However, as the gtmseg.mgz is in the 0.5 mm space, it did give me results after Muller-Gartner PVC without any errors (the mgx.gm file is in the 1mm T1 space), but I am not sure if it is correct or not. Can you help me with this issue? I attached the code I used: mri_gtmpvc \ --i ${PET_smoothed_image_coregistered} \ --seg ${GTMSEG_resampled_to_T1mm} \ --reg-identity \ --default-seg-merge \ --no-reduce-fov \ --mgx .1 \ --psf 6 \ --no-rescale \ --o ${ROI_folder}/${FS_SUBJECT_ID}_gtmpvc_noscale Thanks, Yuheng

2 1

mris_flatten limitations
by Glen, Daniel (NIH/NIMH) [E] 28 Apr '25

28 Apr '25

External Email - Use Caution I would like to abuse mris_flatten with a non-cerebrum surface. Will this work? It works for a sphere, but if I make cuts on more complicated shapes, it fails after hundreds of iterations with a "Segmentation fault". Are there any special tricks? Each patch file of cuts requires a different ?h.smoothwm file or h?.smoothwm file. If I copy the original surface to that requested file, the program continues. Is this correct? How can I predict this? I did manage to get one to make a flat.3D file, but display in Freeview or info from mris_info fails for that output, first using up large amounts of memory then crashes with another segmentation fault . Thanks, Daniel

2 3

Join the mailing list
by Y Zeng 23 Apr '25

23 Apr '25

External Email - Use Caution Tsengyuheng1999(a)gmail.com

1 0

mri_surf2vol error: mri_read(): code inconsistency (file type recognized but not caught)
by Loïc Daumail 20 Apr '25

20 Apr '25

External Email - Use Caution Dear all, I am trying to convert label files into volume ROI masks. This is my command below: mri_surf2vol --surfval /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label --o /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/fonctional_vol_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.nii.gz --identity sub-NSxLxYKx1964 --hemi lh --fillribbon --template /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives/freesurfer/sub-NSxLxYKx1964/mri/brain.mgz I get this error: Reading surface /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives/freesurfer/sub-NSxLxYKx1964/surf/lh.white Done reading source surface Reading thickness /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/derivatives/freesurfer/sub-NSxLxYKx1964/surf/lh.thickness Done INFO: reading /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label as unknown mri_read(): type = 32 error: mri_read(): code inconsistency (file type recognized but not caught) ERROR: could not read /Users/ldaumail3/Documents/research/ampb_mt_tractometry_analysis/ampb/analysis/functional_surf_roi/sub-NSxLxYKx1964/sub-NSxLxYKx1964_hemi-L_space-fsnative_label-MT_mask.label as unknown Any idea what would cause this? Is it because the labels weren't saved in the correct format? Thanks, Best, -Loïc

2 3

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer April 2025