Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

Question on Samseg Basic and Samseg for MS lesions
by Sennott, Liam Ricker 12 May '25

12 May '25

Sent on behalf of Arianna Menardi: ---- Dear Experts, I'm trying to quantify the volume of some white matter lesions in an elderly group. I have tried using both Samseg cross-sectional, as well as Samseg for MS lesions. I am new to the approach so I have 3 main questions: 1. Can I use Samseg for MS lesions even if my patients present WM lesions but are not MS patients? 2. the estimated values of WM-hypointensities derived from the basic version of Samseg are almost half in size compared to the output 'Lesions" of Samseg specific for MS lesions. What is hence the difference between the two approaches that could explain such a big difference in the output? 3. Can I use Samseg combining T1w, FLAIR and SWI data? Or the algorithms are not suited for SWI images? Thank you for your help, Arianna

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Re: [Freesurfer] mri_glmfit error - matrix ill-conditioned. no solution from archive.
by Douglas N. Greve 09 May '25

09 May '25

Not necessarily. This error can arise if any of the columns are linearly dependent. But try rescaling first On 5/9/2025 8:29 AM, Ane Gurtubay wrote: > > External Email - Use Caution > > Dear Douglas, > > whenever we get this error *ERROR: matrix is ill-conditioned or badly > scaled* as in > https://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg74674.html > <https://secure-web.cisco.com/1oJ3YaCat1otNMsv9b4ieBxS300R4fr4eMozJ0nxWe7N3b…>, > should we normalize the values in the fsgd file or the design matrix > (Xg.dat)? > > Thank you in advance, > Ane > > ---- > Ane Gurtubay Antolin, PhD > Ikerbasque Research Fellow > Basque Center on Cognition, Brain and Language (BCBL) > http://www.bcbl.eu/en/ane-gurtubay-antolin > <http://secure-web.cisco.com/10Mht_1YL1Yjet8TT5lrE72xv1nVXLPfSiYFb6jv4xo-YOw…> >

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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

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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.

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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

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Request to Post Job Position on Freesurfer listserv
by Otero Ospina, Andrea 01 May '25

01 May '25

External Email - Use Caution [A close up of a logo Description automatically generated][UGWqtuoMAAAAASUVORK5CYII=] Department of Psychiatry and Behavioral Sciences Postdoctoral Associate Position in Human Neuroimaging University of Miami Miller School of Medicine, Miami, Florida, USA The Gabbay Laboratory within the Department of Psychiatry at the University of Miami Miller School of Medicine is seeking highly motivated postdoctoral scholars in the field of human neuroimaging. Available positions will focus on analyzing fMRI and proton MR spectroscopy data as well as acquiring or processing related MRI and biological measures. Candidates should either have completed or be near completing a PhD in neuroscience, psychology, cognitive neuroscience, radiology, engineering, biostatistics, or a related field, and should have a strong background in quantitative analysis. Proficiencies with at least one major neuroimaging software suite (e.g. FSL, AFNI, SPM, Freesurfer, Caret, Connectome Workbench, etc.) and Unix/Linux environment are expected. Familiarity with Matlab, Python, and/or R programming languages is a plus. The primary responsibilities for this postdoctoral fellow will be to run scans, analyze neuroimaging data from multiple ongoing and recently concluded research projects, and write manuscripts. Under the mentorship of Vilma Gabbay, MD and Benjamin Ely, PhD, postdoctoral scholars will be expected to advance clinical and methodological knowledge through their postdoctoral training. Our lab is dedicated to the study and treatment of mood, anxiety, and substance use disorders in adolescent and high-risk adult (e.g. HIV+) populations using innovative neuroimaging and immunological methodologies. The neuroimaging program features high-resolution data acquisition and analysis techniques modeled on the Human Connectome Project (HCP) and is committed to the highest standards for magnetic resonance imaging and spectroscopy. The lab is funded by four ongoing NIH R01 neuroimaging studies (R01MH120601, R01DA054885, R01MH128878, and R01MH131207) and several smaller grants, providing unparalleled funding for active and exploratory studies. Major research topics include longitudinal studies of adolescent mood and anxiety disorders; comorbidity of depression, cannabis use, and HIV infection; and an intervention study aimed at improving well-being among healthcare workers with parental responsibilities during the COVID-19 pandemic. Project abstracts with further details can be found on NIH RePORTER. Resources available on-campus and through long-standing collaborations include multiple research-dedicated 3T MRI scanners (Siemens Skyra/Vida/Prisma) with cutting-edge accelerated and multi-echo fMRI sequences, high-performance scientific computing clusters, and an extensive library of analytic and statistical software. The PIs are fully committed to fostering the trainee's research independence through publication of first-authored manuscripts in top journals and mentorship in grant applications. In addition to assisting with the PI’s proposals, the successful applicant will be highly encouraged to develop and pursue funding for their own research project through federal (e.g. NIH F32) or foundation grant programs by the end of their first year. Please send a CV, statement of interest, and contact information for three references to axo833(a)med.miami.edu<mailto:axo833@med.miami.edu>. All qualified candidates will be given equal consideration. Priority will be given to candidates available to start sooner. Compensation will be proportional to experience and will follow standard postdoctoral fellowship rates posted by University of Miami. Andrea Otero, M.D. Clinical Research Laboratory Supervisor Department of Psychiatry and Behavioral Sciences University of Miami — Miller School of Medicine Email: axo833(a)med.miami.edu<mailto:njh115@med.miami.edu> Phone: 305-243-7086 [Image]

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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

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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

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Join the mailing list
by Y Zeng 23 Apr '25

23 Apr '25

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

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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

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