Freesurfer

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30084 discussions

Research Study Support
by Kasperek, Jessica 15 Jul '26

15 Jul '26

External Email - Use Caution Hello, One of my research studies, a retrospective Multiple Sclerosis (MS) study, is looking to conduct analyses on volumetric changes in brain MRI scans of MS patients during the course of their treatment. Specifically, it is looking for these items: * Overall brain volume change * Total lesion load * Cervical spine lesion * New MRI lesions * Asymmetrical atrophy between left and right hemispheres * Hippocampus * Thalamus * Basal ganglia * Prefrontal cortex * Cerebellum * Cortical GM Each patient has approx. 10 MRI scans or so. Is this a doable project for FreeSurfer? Any recommendations on how to approach this with the software? Any help is appreciated as there is no one at my institution that could direct me with the appropriate steps. Thanks, Jessica ******************* PLEASE NOTE ******************* This message and any documents accompanying this transmission may contain information that is privileged, confidential, and/or exempt from disclosure under applicable law and is intended solely for the addressee(s) named above. If you are not the intended addressee/recipient, you are hereby notified that any use of, disclosure, copying, distribution, or reliance on the contents of this message is strictly prohibited and may result in legal action against you. Please reply to the sender advising of the error in transmission and immediately delete/destroy the message and any accompanying documents. Thank you.

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Differences between mri_surf2surf and mris_ca_label for cortical parcellation
by Alex 15 Jul '26

15 Jul '26

External Email - Use Caution Dear experts, As far as I know, there are two common ways to assign anatomical labels to cortical vertices: using mri_surf2surf (combined with an atlas annot file) and using mris_ca_label (which relies on a pre-trained classifier). My question is: in practice, which method is preferable? Is mris_ca_label theoretically more accurate, but in reality the two yield nearly identical results? Or are there systematic, non-negligible differences? Also, is mris_ca_label less robust than the simpler projection method, particularly in subjects with imperfect surface reconstruction. Thank you for your advice. Yang Hu

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Choroid plexus volumes zeroed out in aseg.stats
by Chholak, Parth (NIH/NIAAA) [F] 14 Jul '26

14 Jul '26

External Email - Use Caution Hello FreeSurfer Developers, I need to compute volumes of different brain regions using T1 MPRAGE MRIs, and the standard approach of running `recon-all`, followed by `asegstats2table` is working fine for most regions. However, in some cases, the volumes are either zeroed out (e.g., for choroid plexus) or missing altogether (e.g., for habenula), and I am wondering what is the recommended approach to calculate volumes in these cases. Should I create a new segmentation volume manually on top of fsaverage that is aligned to my subject MRIs and run `mri_segstats`, or should I use `mri_synthseg`? Adding FreeSurfer and computer info in case it is helpful: * FreeSurfer version: `freesurfer-linux-centos7_x86_64-8.2.0-20260314-d932c45` * Platform: CentOS Linux 7 (Core) Thank you in advance, Robin Parth Chholak, Ph.D. Clinical NeuroImaging Research Core National Institute on Alcohol Abuse and Alcoholism National Institutes of Health Phone: +1 (301) 594-7416

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FS 8.0.0 Symlink Bug: Continue With 8.0.0 or Switch to 8.1.0/8.2.0 After Manual Edits?
by Lubig, Andreas 13 Jul '26

13 Jul '26

External Email - Use Caution Hello, I am working with a longitudinal dataset that was initially processed entirely with FreeSurfer 8.0.0. The cross-sectional time points were manually edited and then rerun with FreeSurfer 8.0.0. The base subjects and longitudinal subjects were also created with 8.0.0. I am now at the stage where I may need to manually edit the base subjects and possibly the longitudinal subjects, and I am unsure which FreeSurfer version I should use for the remaining edits and reruns. My concern is the documented FreeSurfer 8.0.0 bug in which rerunning recon-all can turn mri/orig.mgz into a symbolic link to mri/nu.mgz, particularly after manual editing and rerunning the processing. As far as I can tell, this bug did not occur in my dataset. I checked all relevant directories recursively and found no orig.mgz symbolic links and no cases in which orig.mgz and nu.mgz were byte-for-byte identical. My questions are: 1. Since the cross-sectional subjects were already manually edited and rerun with FreeSurfer 8.0.0, should I continue using 8.0.0 for manual edits and reruns of the base and longitudinal subjects in order to keep the processing version consistent, while checking that the symbolic-link error does not occur? 2. Alternatively, since it would take too much time to do all the manual edits all over again, can I keep the existing cross-sectional subjects and switch to a newer FreeSurfer version for the base and longitudinal processing? 3. If I should switch, would you recommend FreeSurfer 8.1.0 or 8.2.0? 4. Would it be acceptable to keep the existing base subjects created with 8.0.0 and use FreeSurfer 8.1.0 or 8.2.0 only for editing and rerunning the base and longitudinal subjects? Or should I first recreate the base subjects with 8.1.0 or 8.2.0 and only then begin the manual editing? I also have a separate question about the longitudinal results. Is it expected or possible that: * the cross-sectional subject looks correct after editing and rerunning, * the base subject also looks correct, * but the corresponding longitudinal subject contains pial-surface errors that are not present in either the cross-sectional or base subject? The longitudinal subjects look worse than the edited and rerun cross-sectional subjects and also worse than the base subjects. The study period was about one year, with two to three MRI sessions per participant. I observed this both in adolescent participants with anorexia nervosa who gained weight over the one-year period (and in whom substantial brain volume changes would be expected), and in adolescent healthy controls (in whom normal developmental brain changes are also expected). Could it indicate that something went wrong during the creation of the longitudinal subjects? If so, what is the most likely cause? Thank you very much for your help! Best regards, Andreas

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Question Regarding Synth Tools for Quantitative Atrophy Analysis
by John Anderson 10 Jul '26

10 Jul '26

External Email - Use Caution Hello, Could an expert in the Synth collection of tools please confirm whether these tools are intended for reliable use in patient populations, or primarily in healthy brains? Specifically, we would like to understand whether the Synth tools can preserve and reproduce cortical atrophy measurements in a manner comparable to the full recon-all pipeline. Practically, it appears that recon-all and the Synth tools may produce different measurements for the same brains, so we would like to clarify the expected use case. For example, if we have a pooled MRI dataset from patients with different neurological pathologies, including Alzheimer’s disease, amyotrophic lateral sclerosis, and other disorders, each condition may have a distinct cortical atrophy pattern. Are the Synth tools able to perform segmentation while preserving these disease-specific pathological patterns, or should they not be used for quantitative atrophy analysis? Any advice would be appreciated. Thank you. John

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SuperSynth Method and Longitudnal Analysis
by Ajay Sharma 09 Jul '26

09 Jul '26

External Email - Use Caution Dear Team, We are currently using the new SuperSynth method to process and segment 3T T1-weighted MRI volumes acquired at three longitudinal time points (Baseline, Visit 1, and Visit 2). We would like to know whether it is possible to perform a longitudinal analysis using the outputs generated by SuperSynth. If so, could you please describe the recommended workflow or commands to follow? Specifically, we are interested in the following: * Can SuperSynth outputs be used for longitudinal processing across multiple time points? * Is there a recommended pipeline or set of commands for longitudinal analysis? * Can we generate cortical thickness measurements and cortical thickness maps to visualize brain changes over time? * Are there any additional recommendations or best practices for performing longitudinal structural analyses using SuperSynth, SynthSeg or recon-all-clinical outputs? Any suggestions, documentation, or example of workflows would be greatly appreciated. Thank you for your time and assistance. Best, Ajay

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Re: fiducials_calibration error: failed to start python script
by fsbuild 07 Jul '26

07 Jul '26

External Email - Use Caution I'm not familiar with that code, but in my 8.2.0 install under /Applications/freesurfer/8.2.0/bin/dissection_photo there is a dissection_photo_gui.sh script which looks like it is expected to be run in the freesurfer environment.   So perhaps the PhotoTools WIKI page under the section Dissection Photo GUI should have listed dissection_photo_gui.sh instead of dissection_photo_gui. - R. On 7/7/26 06:43, Andy Choi (andy.choi.24(a)ucl.ac.uk) wrote:         External Email - Use Caution         Hello FreeSurfer developers,  I'm trying to use the PhotoTools workflow described here: https://secure-web.cisco.com/1S5KZ0alyS3_qJzmuz3eanZ5ZGaTPDRjDTccnIZ01h_W3c… When I run fiducials_calibration on macOS, the GUI opens and I am able to select the photos and select markers, but it then immediately reports "failed to start Python script".  I tested both FreeSurfer 8.1.0 and 8.2.0 ARM64 installations and saw the same issue. After inspecting, it looks like it is looking for func_fiducials_calibration.py. However, this file does not seem to be anywhere under FREESURFER_HOME.  I also noticed that dissection_photo_gui is not available in the installed package either. I have tried cloning the FreeSurfer GitHub repository and found the missing scripts there but haven't been able to run them without the GUI. Could you please let me know whether PhotoTools is currently supported in the macOS ARM64 release, and whether there are steps I am currently missing in terms of installation? FreeSurfer version: freesurfer-macOS-darwin_arm64-8.1.0-20250718-f30dfed Also tested: freesurfer-macOS-darwin_arm64-8.2.0-20260314-d932c45 Platform: macOS (M3) Darwin MacBook-Pro-95.powerhub 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:30:59 PST 2023; root:xnu-10002.81.5~7/RELEASE_ARM64_T6030 arm64 Relevant output: $ which fiducials_calibration /Applications/freesurfer/8.1.0/bin/fiducials_calibration $ which dissection_photo_gui dissection_photo_gui not found $ find "$FREESURFER_HOME" $ -name "func_fiducials_calibration.py" -o -name "func_fiducials_correction.py" -iname "*dissection_photo*" $ -print [no output] $ fiducials_calibration WARNING: Secure coding is not enabled for restorable state... "Failed to start python script" Thank you! _______________________________________________ Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.edu To unsubscribe send an email to freesurfer-leave(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1j7MsnMzpw-5ZWBQehMY_o_tvDufHv9ueix2D1kYZtTzue… The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1fbIx-iN6s2714OiZv1ybt7qZzQNL8OcGLrMsV1Ve8II3C… <https://secure-web.cisco.com/1Brn1dBph_8fuZRjMgLBk0JT_olLSVugwQ1U2A3RgKqz8J_u-GRgUCRtXhLI-yRhqMLbBbZWPj9HOS8DeDUiUBd-kGHqcix6OwR6T3QkgP2ZFeB7yR8sJkqOFcfaDpNLiSxheqzt0YVfzX9jD28HDTqipCkCOWZX2_0GTvskd3GxCtcAx40A8yRT42GSWaDZ9owiJomBKfxEg-1jKRO39LxNryAqQ3Fy6Fh2x2kUQSqKhUpMkzrjTBGoRTnD02onuIyULqRmKNtjewMGYMjgCR4aMg2BFbC03ocDx9gr-C_txpZKty9g-jTUCtXhNZUAqpIKkxCPV87OTQGFfnENiLw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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fiducials_calibration error: failed to start python script
by Andy Choi 07 Jul '26

07 Jul '26

External Email - Use Caution Hello FreeSurfer developers, I'm trying to use the PhotoTools workflow described here: https://secure-web.cisco.com/1f0JHfoKVyitXKFbtrfb2mHr5U9i83u-MdcT2voziN6ZmR…<https://secure-web.cisco.com/1ht75mQag4ubHK8uSY51Oi4Zgdcltw8NMESb59S5n2XFbL…> When I run fiducials_calibration on macOS, the GUI opens and I am able to select the photos and select markers, but it then immediately reports "failed to start Python script". I tested both FreeSurfer 8.1.0 and 8.2.0 ARM64 installations and saw the same issue. After inspecting, it looks like it is looking for func_fiducials_calibration.py. However, this file does not seem to be anywhere under FREESURFER_HOME. I also noticed that dissection_photo_gui is not available in the installed package either. I have tried cloning the FreeSurfer GitHub repository and found the missing scripts there but haven't been able to run them without the GUI. Could you please let me know whether PhotoTools is currently supported in the macOS ARM64 release, and whether there are steps I am currently missing in terms of installation? 1. FreeSurfer version: freesurfer-macOS-darwin_arm64-8.1.0-20250718-f30dfed Also tested: freesurfer-macOS-darwin_arm64-8.2.0-20260314-d932c45 2. Platform: macOS (M3) 3. Darwin MacBook-Pro-95.powerhub 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:30:59 PST 2023; root:xnu-10002.81.5~7/RELEASE_ARM64_T6030 arm64 4. Relevant output: $ which fiducials_calibration /Applications/freesurfer/8.1.0/bin/fiducials_calibration $ which dissection_photo_gui dissection_photo_gui not found $ find "$FREESURFER_HOME" $ -name "func_fiducials_calibration.py" -o -name "func_fiducials_correction.py" -iname "*dissection_photo*" $ -print [no output] $ fiducials_calibration WARNING: Secure coding is not enabled for restorable state... "Failed to start python script" Thank you!

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Research Study Question - FreeSurfer Use
by Kasperek, Jessica 05 Jul '26

05 Jul '26

External Email - Use Caution Hello, One of my research studies, a retrospective Multiple Sclerosis (MS) study, is looking to conduct analyses on volumetric changes in brain MRI scans of MS patients during the course of their treatment. Specifically, it is looking for these items: * Overall brain volume change * Total lesion load * Cervical spine lesion * New MRI lesions * Asymmetrical atrophy between left and right hemispheres * Hippocampus * Thalamus * Basal ganglia * Prefrontal cortex * Cerebellum * Cortical GM Each patient has approx. 10 MRI scans or so. Is this a doable project for FreeSurfer? Any recommendations on how to approach this with the software? Any help is appreciated. Thanks, Jessica Jessica Kasperek Research Coordinator Neurology Department - Clinical Research Unit 1 Endeavor Health 2650 Ridge Avenue, Burch Building Room 310, Evanston, IL 60201 (p) 847-570-1864 (e) jessica.kasperek(a)endeavorhealth.org [cid:b190731c-8276-47fe-a322-7bde2a6cf3c8] ******************* PLEASE NOTE ******************* This message and any documents accompanying this transmission may contain information that is privileged, confidential, and/or exempt from disclosure under applicable law and is intended solely for the addressee(s) named above. If you are not the intended addressee/recipient, you are hereby notified that any use of, disclosure, copying, distribution, or reliance on the contents of this message is strictly prohibited and may result in legal action against you. Please reply to the sender advising of the error in transmission and immediately delete/destroy the message and any accompanying documents. Thank you.

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infant_recon_all: could not open aseg.16.mgz
by Dierker, Donna 02 Jul '26

02 Jul '26

External Email - Use Caution Hi infant freesurfer gurus, I need help with infant_recon_all. I have existing third-party segmentations for six month old babies' T1w's. I have relabeled them with label indices that bibsnet would output. Then I tried running nibabies like so: docker run --rm -i -u 1697:10 -v /usr/local/pkg/freesurfer7.3/.license:/opt/freesurfer/license.txt:ro -v /my_file_system/rawdata:/data:ro -v /my_file_system/derivatives/nibabies:/out -v /my_file_system/work/nibabies/sub-01:/work -v /my_file_system/derivatives/bibsnet:/deriv1 nipreps/nibabies:25.2.1 /data /out participant --participant-label 01 -s 6mo -w /work --verbose --derivatives /deriv1 --anat-only --fd-spike-threshold 0.2 --age-months 6 --surface-recon-method infantfs --cifti-output 91k --debug registration --project-goodvoxels --multi-step-reg --norm-csf --omp-nthreads 8 --mem 300000 --nprocs 8 --stop-on-first-crash --output-spaces fsLR MNIInfant:cohort-3 MNI152NLin6Asym:res-2 anat It runs 30-60 minutes and seems to make some surfaces before bailing like so: writing spherical brain to /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/surf/lh.qsphere.nofix spherical transformation took 0.0770 hours FSRUNTIME@ mris_sphere 0.0770 hours 8 threads #VMPC# mris_sphere VmPeak 929720 mris_sphere done /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/surf /work/nibabies_26_0_wf/single_subject_sub-01_ses-6mo_wf/infant_single_t1w_fit_wf/infantfs_surface_recon_wf/reconall cp /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/surf/lh.qsphere.nofix lh.qsphere.nofix cp /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/surf/rh.qsphere.nofix rh.qsphere.nofix /work/nibabies_26_0_wf/single_subject_sub-01_ses-6mo_wf/infant_single_t1w_fit_wf/infantfs_surface_recon_wf/reconall mri_or /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/aseg.right.41.mgz /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/aseg.left.2.mgz /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/wo rk/aseg.16.mgz /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/wm.nonscaled.mgz processing 3 input files processing input volume 1 of 3: /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/aseg.right.41.mgz processing input volume 2 of 3: /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/aseg.left.2.mgz processing input volume 3 of 3: /out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/aseg.16.mgz error: mghRead(/out/sourcedata/freesurfer/sub-01_ses-6mo/work/sub-01_ses-6mo/work/aseg.16.mgz, -1): could not open file Segmentation fault (core dumped) I suspect aseg.16.mgz is the Brain-Stem, and these third-party segmentations did not separate the brainstem into pons, medulla, and midbrain, so I left the brainstem unlabeled. But after running into this issue, I tried relabeling the brainstem to label index 16 and ran nibabies again -- same error. I have been looking at these web pages for possible work-arounds, but I could use some help, if you have any ideas: https://secure-web.cisco.com/1kXsEAk5LcnODg46NZQ42ThUNHIoft_7-54OwfS8OeJsNP… https://secure-web.cisco.com/1E2XdEVYlFV-azzD0J4zRpK1RYhrDPSVxPfxg3Eqx3SHiC… Sorry for the long message and odd question, but as you know this timepoint is very challenging, and the segmentations are otherwise promising. Thank you for any ideas you have for working around this issue, Donna ________________________________ 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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