Freesurfer March 2025

freesurfer@nmr.mgh.harvard.edu

49 participants
63 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

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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

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LME ROI group analysis
by Bondi, Daniel 16 Apr '25

16 Apr '25

External Email - Use Caution Hi FreeSurfer experts, I am using the univariate LME pipeline (lme_fit_FS & lme_F) to conduct cortical thickness analysis on a subset of D-K atlas ROIs between two groups. Although I am testing longitudinal group*time differences with this pipeline, I am wondering if it is valid to test group-level differences (irrespective of time) with this model as well. I have been doing so by specifying only the group covariate in the contrast matrix before running the model. Thank you, Daniel Bondi

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Problem with aparcstats2table
by Rosalia Dacosta Aguayo 15 Apr '25

15 Apr '25

External Email - Use Caution Dear Freesurfer team, I am having a trouble with aparcstats2table I have never seen before and I do not know how to solve it. I have run it with --help and still I don't quite understand it. Any help would be appreciated. Kind regards, Rosie rosalia@rosalia-Lenovo-Y520-15IKBN:~/Desktop/CAN_RUTI$ aparcstats2table --hemi rh --subjects sub-012_ses-BSL sub-012_ses-FU1 sub-012_ses-FU2 sub-013_ses-BSL sub-013_ses-FU1 sub-013_ses-FU2 sub-014_ses-BSL sub-014_ses-FU1 sub-014_ses-FU2 sub-015_ses-BSL sub-015_ses-FU1 sub-015_ses-FU2 sub-016_ses-BSL sub-017_ses-BSL sub-017_ses-FU1 sub-017_ses-FU2 sub-019_ses-BSL sub-019_ses-FU1 sub-019_ses-FU2 sub-020_ses-BSL sub-020_ses-FU1 sub-020_ses-FU2 sub-021_ses-BSL sub-021_ses-FU1 sub-021_ses-FU2 sub-022_ses-BSL sub-022_ses-FU1 sub-022_ses-FU2 sub-023_ses-BSL sub-023_ses-FU1 sub-023_ses-FU2 sub-024_ses-BSL sub-024_ses-FU1 sub-024_ses-FU2 sub-025_ses-BSL sub-028_ses-BSL sub-028_ses-FU1 sub-029_ses-BSL sub-029_ses-FU1 sub-029_ses-FU2 sub-030_ses-BSL sub-030_ses-FU1 sub-030_ses-FU2 sub-031_ses-BSL sub-031_ses-FU1 sub-031_ses-FU2 sub-032_ses-BSL sub-032_ses-FU2 sub-033_ses-BSL sub-033_ses-FU1 sub-033_ses-FU2 sub-034_ses-BSL sub-034_ses-FU1 sub-035_ses-BSL sub-035_ses-FU1 sub-035_ses-FU2 sub-036_ses-BSL sub-036_ses-FU1 sub-036_ses-FU2 sub-037_ses-BSL sub-038_ses-BSL sub-038_ses-FU1 sub-038_ses-FU2 sub-039_ses-BSL sub-039_ses-FU1 sub-039_ses-FU2 sub-040_ses-BSL sub-040_ses-FU1 sub-040_ses-FU2 sub-041_ses-BSL sub-041_ses-FU1 sub-041_ses-FU2 sub-042_ses-BSL sub-042_ses-FU1 sub-043_ses-BSL sub-044_ses-BSL sub-045_ses-BSL sub-046_ses-BSL sub-046_ses-FU1 sub-046_ses-FU2 sub-047_ses-BSL sub-047_ses-FU1 sub-047_ses-FU2 sub-048_ses-BSL sub-051_ses-BSL sub-051_ses-FU1 sub-051_ses-FU2 sub-053_ses-BSL sub-054_ses-BSL sub-054_ses-FU1 sub-054_ses-FU2 sub-055_ses-BSL sub-055_ses-FU1 sub-056_ses-BSL sub-056_ses-FU1 sub-056_ses-FU2 sub-057_ses-BSL sub-058_ses-BSL sub-058_ses-FU1 sub-058_ses-FU2 sub-059_ses-BSL sub-060_ses-BSL sub-060_ses-FU1 sub-060_ses-FU2 sub-061_ses-BSL sub-061_ses-FU1 sub-061_ses-FU2 sub-062_ses-BSL sub-062_ses-FU2 sub-063_ses-BSL sub-064_ses-BSL sub-064_ses-FU1 sub-064_ses-FU2 sub-065_ses-BSL sub-065_ses-FU1 sub-065_ses-FU2 sub-067_ses-BSL sub-068_ses-BSL sub-068_ses-FU1 sub-068_ses-FU2 sub-069_ses-BSL sub-070_ses-BSL sub-070_ses-FU1 sub-070_ses-FU2 sub-071_ses-BSL sub-072_ses-BSL sub-072_ses-FU1 sub-072_ses-FU2 sub-073_ses-BSL sub-074_ses-BSL sub-074_ses-FU1 sub-074_ses-FU2 sub-075_ses-BSL sub-075_ses-FU1 sub-075_ses-FU2 sub-076_ses-BSL sub-077_ses-BSL sub-077_ses-FU1 sub-077_ses-FU2 sub-078_ses-BSL sub-079_ses-BSL sub-079_ses-FU1 sub-079_ses-FU2 sub-080_ses-BSL sub-080_ses-FU1 sub-080_ses-FU2 sub-081_ses-BSL sub-082_ses-BSL sub-082_ses-FU1 sub-082_ses-FU2 sub-083_ses-FU1 sub-083_ses-FU2 sub-084_ses-BSL sub-084_ses-FU1 sub-084_ses-FU2 sub-085_ses-BSL sub-085_ses-FU1 sub-085_ses-FU2 sub-086_ses-BSL sub-086_ses-FU1 sub-086_ses-FU2 sub-087_ses-BSL sub-087_ses-FU1 sub-087_ses-FU2 sub-088_ses-BSL sub-088_ses-FU1 sub-088_ses-FU2 sub-089_ses-BSL sub-089_ses-FU1 sub-089_ses-FU2 sub-090_ses-BSL --meas thickness --tablefile aparc-stats-thickness.txt *ERROR: Specify one of --subjects, --subjectsfile --qdec or --qdec-long* or run with --help for help. ____________________________________________________________________________ Aquest missatge, i els fitxers adjunts que hi pugui haver, pot contenir informació confidencial o protegida legalment i s’adreça exclusivament a la persona o entitat destinatària. Si no consteu com a destinatari final o no teniu l’encàrrec de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si l’heu rebut per error, informeu-ne el remitent i elimineu del sistema tant el missatge com els fitxers adjunts que hi pugui haver. Este mensaje, y los ficheros adjuntos que pueda incluir, puede contener información confidencial o legalmente protegida y está exclusivamente dirigido a la persona o entidad destinataria. Si usted no consta como destinatario final ni es la persona encargada de recibirlo, no está autorizado a leerlo, retenerlo, modificarlo, distribuirlo o copiarlo, ni a revelar su contenido. Si lo ha recibido por error, informe de ello al remitente y elimine del sistema tanto el mensaje como los ficheros adjuntos que pueda contener. This email message and any attachments it carries may contain confidential or legally protected material and are intended solely for the individual or organization to whom they are addressed. If you are not the intended recipient of this message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any part of it. If you have received the message by mistake, please inform the sender of this and eliminate the message and any attachments it carries from your account.

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trac-preproc: orientLAS and mri_info issue with unsigned shorts
by Mirro, Amy 11 Apr '25

11 Apr '25

External Email - Use Caution Hi, Thanks so much for all your work on Freesurfer. I am currently running tracula v7.4 and I am coming across the following error. I believe this error is occurring during the orientLAS call in trac-preproc (the output is copied from my log file): orientLAS /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig.1.nii.gz /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig_las.1.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8 awk: cannot open is (No such file or directory) awk: cannot open is (No such file or directory) awk: cannot open is (No such file or directory) mri_convert -oni INFO: -onj This -onk is -oid inf 0 0 -ojd -inf 0 0 -okd inf 0 0 -oc -rt nearest /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig.1.nii.gz /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig_las.1.nii.gz mri_convert -oni INFO: -onj This -onk is -oid inf 0 0 -ojd -inf 0 0 -okd inf 0 0 -oc -rt nearest /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig.1.nii.gz /storage1/fs1/fields_m/Active/Scanner_Update_DTI_Testing/PROTO1_3_k23/dmri/dwi_orig_las.1.nii.gz I think the error in orientLAS might be due to the mri_info calls inside orientLAS (starting around here: https://secure-web.cisco.com/1yGfA9jbEQb9uMtyDf5LggAJmO-aUQoPIO34H0YN-0Lu0i…) When I attempt to run mri_info on my niftis, I get the following warning : "INFO: this is an unsiged short. I'll try to read it, but it might not work if there are values over 32k -1 -0 0" I think that when mri_info returns this warning inside the orientLAS code, it causes orientLAS to fail, since the xyzR, xyzA, and xyzS variables are not set as expected. Do you have any suggestions on how I could solve this? Is there perhaps a way to suppress the warning in mri_info? Or is there a straightforward way to convert unsigned short data? Thanks, Amy ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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mris_register external atlas
by Stefanie Bradley 10 Apr '25

10 Apr '25

External Email - Use Caution Hi there, I am trying to register my Freesurfer subject's cortical surface into a common space to use the parcellations from a pediatric atlas (UNC 4D cortical surface atlas). With Freesurfer version 8.0.0 in a Linus OS, I am using mris_register as: mris_register -1 individual_subject/lh.sphere 4D_atlas/lh.sphere individual_subject /lh.sphere.FS.reg. I am getting an error where it says it requires a smoothwm file from the atlas files, though I only have curvature and sphere files from the atlas. Is there a way to register the atlas files to my subjects and then put the parcellations onto my subject's cortical surface? Thanks, Stefanie

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Error using -nonuintensitycor
by Jeffrey Spielberg 07 Apr '25

07 Apr '25

External Email - Use Caution Hello, I'm running Freesurfer 8.0.0 on a Rocky machine and run into an error when I use the -nonuintensitycor flag. The same image finels run perfectly fine without that flag, but with the flag I get this error: #@# Intensity Normalization Tue Mar 18 15:22:23 EDT 2025 /s3l/fs_subjects/RAD_2100A/mri mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading mri_src from nu.mgz... error: mghRead(/s3l/fs_subjects/RAD_2100A/mri/nu.mgz, -1): could not open file^@ error: mri_normalize: could not open source file nu.mgz^@ Command exited with non-zero status 255 This looks to be a bug - any ideas for a workaround? Thanks! -- Jeffrey M. Spielberg, Ph.D. Associate Professor, Clinical Science Department of Psychological and Brain Sciences University of Delaware, Newark, DE 19716 Office: 344 Building X Lab: Suite 302 Building X Email: jmsp(a)udel.edu Web: http://secure-web.cisco.com/1kOZT8vAxRUMrcZR3lkwUFNSIHUk1cRyGyu1QIlfYEHDpjV… Personal Zoom: https://secure-web.cisco.com/1PQ64OpYtuV98rydOWj5-yZN6p9Fy4OUwzLD2N9sfyBBF7… Please be aware that e-mail communication can be intercepted in transmission or misdirected. Please consider communicating any sensitive information by telephone, fax, or mail. The information contained in this message may be privileged and confidential. If you are NOT the intended recipient, please notify the sender immediately and destroy this message.

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samseg: unrecognized flag with --lesion-mask-pattern
by Simone Cauzzo 07 Apr '25

07 Apr '25

External Email - Use Caution Dear support I'm running samseg using Freesurfer 7.4.0. I'm using t1, t2 and flair as input. I'm not sure if it's necessary to specify --lesion-mask-pattern but if I try, I get an unrecognized flag error as it reads the second input to --lesion-mask-pattern as a new flag. Log: ERROR: Flag 1 unrecognized. --t1w [...]/001.mgz --flair [...]/oFL.mgz --t2w [...]/oT2.mgz --s [...]01 --recon --use-flair --refmode t1w --pallidum-separate --lesion --fill --threads 16 --lesion-mask-pattern 0 1 1 if I remove the "--lesion-mask-pattern 0 1 1" I don't get any error. Any suggestion? Thanks Simone

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Importing surface meshes from 3rd party cortical surface reconstruction tools for analysis in fsaverage template space
by James Hengenius 03 Apr '25

03 Apr '25

External Email - Use Caution Hi, I'm working with infant (0-30 month) MR data, and iBEAT ( https://secure-web.cisco.com/1T2WKIelhUu8n_wuNR_5gb37RydVg1xrWEVvlUOdcz2UFW…) is currently doing a better job than Infant FreeSurfer ( https://secure-web.cisco.com/1M3VIitCZu3azJ0yMsnC2UvSxSyhcRAkbfTg_v1IUkOJOb…) at cortical surface recon in this age range. However, I have custom surface ROI atlases on the fsaverage template and would very much like to leverage FreeSurfer's stats tools to map iBEAT subject surfaces to the template and extract stats from my custom ROIs. To do so, I need to - Bring my iBEAT VTK surfaces (~47K vertices per hemisphere) into FreeSurfer (mris_convert?) - Resample the meshes to FS surface resolution (~12.5K vertices per hemi) - Compute curvature stats on the iBEAT surfaces - Use mris_surf2surf (or equivalent) to map the resampled iBEAT surface to the fsaverage template using curvature - Compute/extract anatomical stats from the regions equivalent to the ROIs in my template space atlas. All of the above are presenting challenges. So far, I tried using mris_convert to bring the VTK into FS format, but when I tried using mris_anatomical_stats, I get errors. Note that I also ran InfantFS on the data, and that I copied the converted (but not downsampled) VTK pial surface from iBEAT to $SUBJECTS_DIR/$subjid/surf/lh.ibeat.pial > mris_anatomical_stats -log test.ibeat.log sub-0001 lh ibeat.pial outputting results to test.ibeat.log... reading volume /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/mri/wm.mgz... reading input surface /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.ibeat.pial... Using TH3 vertex volume calc Total face volume 58098.7 Total vertex volume 57390.1 (mask=0) reading input pial surface /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.pial... error: mrisReadTriangleFile opened /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.pial okay but surface doesn't match /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.ibeat.pial. nvertices:46854 != mris->nvertices:12240 || nfaces:93704 != mris->nfaces:24476 error: mrisReadTriangleFile failed. error: mris_anatomical_stats: could not read surface file /scratch/t/tpaus/jhengeni/iBEAT/surface_remapping/sub-0001/sub-0001/surf/lh.pial It appears this approach is failing due to a difference in meshes (the iBEAT mesh is at a different resolution, with more elements, than the lh.pial from InfantFS). Any tips for this and the other steps would be a big help! Thanks, Jim H. -- Jim Hengenius Research Associate Paus Research Group CHU Sainte-Justine Research Centre My Google Calendar <http://secure-web.cisco.com/1NyYdK1uBklqcDSsFMhBiedpJnPC-H6m83iYBtfLt-c-oKz…>

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Freesurfer Question - Pediatric pathology
by Stefanie Bradley 02 Apr '25

02 Apr '25

External Email - Use Caution Hi there, I'm working with MRI scans from children aged 3-6 years old. I was wondering if there's a way to integrate pediatric atlases into the Freesurfer recon-all pipeline? I'm also wondering if it's possible to integrate a lesion mask into the pipeline in the case of brain pathology? Thanks, Stef STEFANIE BRADLEY PHD CANDIDATE Holland Bloorview Kids Rehab Hospital 150 Kilgour Rd, Toronto, ON M4G 1R8 stefanie.bradley(a)mail.utoronto.ca [https://secure-web.cisco.com/1kWf2c8NzM8OclMTRcmltfW5rxRU9SRJI50sUcXDGlWqWx…]<https://secure-web.cisco.com/1uQzm_CoDmutDkOsJunQufG19PQx4c0AZhVnSO28l9XE9i…>

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Freesurfer March 2025