Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30128 discussions

mri_gtmpvc --rbv segmentation fault
by Finn, Quentin 22 Jan '26

22 Jan '26

External Email - Use Caution Freesurfer Experts, I am trying to run mri_gtmpvc with the --rbv option, but am unable to progress, I always get a simple error immediately upon running: Segmentation fault (core dumped) The command I am running is this: mri_gtmpvc --i FS_SPACE_pet.nii --reg-identity --psf 3.5 --no-rescale --seg ${SUBJECTS_DIR}/subject1/mri/gtmseg.mgz --default-seg-merge --auto-mask 1 .01 --o subject1_gtmpvcRBV.output --rbv Things I have tried: 1. If I remove the --rbv tag, the command runs as expected. 2. If I run with the --rbv-res option, I still receive the error, even if I set the voxel resolution to a huge value e.g. 8 or 16. 3. My local machine has 32gb of RAM. If I try to run the command on our HPC cluster, I get the same error even when requesting 128gb of memory and 8 threads, using --threads 8. I am running freesurfer-linux-centos7_x86_64-7.4.1-20230613-7eb8460 on RHEL 9. The HPC cluster may have a slightly different version but has the same behavior. Any thoughts on what I might be doing wrong here? Thanks so much! Houston Methodist. Leading Medicine. Houston Methodist Hospital has been named the Best Hospital in Texas for patient care and quality for the 14th year in a row by U.S. News & World Report. We are proud to be a top-ranked hospital in the country, and nationally ranked in 10 specialties. For more than 100 years, we have been honored to provide you with the highest quality care possible. That’s the difference between practicing medicine and leading it. For you. houstonmethodist.org<https://secure-web.cisco.com/1KTL7A4yEQ5clPW8oZVvsq9QYrOmDR-YQLqrx4-VSB3l6w…> x.com/MethodistHosp<https://secure-web.cisco.com/163MCj27y4cYACfAhgyJ_wYOBv5wLUh36rxTuuAh2HNdBx…> facebook.com/HoustonMethodist<https://secure-web.cisco.com/1WtFhEzwI7gPA7DJiQN5d3z6iprygJQ-FEn-Kw4R5WzhhO…> ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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TRACULA error: Could not find thalamic nuclei segmentation despite present
by Simone Cauzzo 22 Jan '26

22 Jan '26

External Email - Use Caution Dear support I'm running the following command in Freesurfer 7.4: trac-all -nocorr -noqa -intra -tensor -inter -prior -debug -dontrun -c config_tracula.txt I get the following error ERROR: Could not find thalamic nuclei segmentation in /nfsd/biopetmri4/Users/CauzzoOPA/FS_RECON/subjOPAPD01/mri/ ERROR: Thalamic nuclei segmentation is strongly recommended to use ERROR: for tracts that terminate in or travel near the thalamus ERROR: If there is good reason not to use it, set usethalnuc = 0 And this happens despite in that folder there are these files: thal_t1_fl.FSspace.mgz thal_t1_fl.thalamus.t2.stripped.bfcorr.mgz thal_t1_fl.thalamus.t2.mgz ThalamicNuclei.v13.thal_t1_fl.FSvoxelSpace.mgz ThalamicNuclei.v13.thal_t1_fl.volumes.txt ThalamicNuclei.v13.thal_t1_fl.mgz then why isn't it finding the thalamic segmentation? I paste below the full output of the command Thank you ###################################### INFO: SUBJECTS_DIR is /nfsd/biopetmri4/Users/CauzzoOPA/FS_RECON INFO: Diffusion root is /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res Actual FREESURFER_HOME /nfsd/opt/FSL/freesurfer-7.4.0 trac-preproc -c /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/scripts/dmrirc.local -log /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/scripts/trac-all.log -cmd /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/scripts/trac-all.cmd -dontrun -debug INFO: -dontrun flag is in effect so subsequent commands may not have accurate arguments! #------------------------------------- /nfsd/opt/FSL/freesurfer-7.4.0//bin/trac-preproc #------------------------------------- #@# DWI set selection Thu Jan 22 11:38:27 CET 2026 ln -sf dwi.nii.gz /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dmri/data.nii.gz ln -sf dwi.bvecs /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dmri/bvecs ln -sf dwi.bvals /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dmri/bvals #------------------------------------- #@# Intra-subject registration Thu Jan 22 11:38:27 CET 2026 bbregister --s subjOPAPD01 --init-fsl --dti --6 --mov /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dmri/lowb.nii.gz --reg /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dmri/xfms/diff2anatorig.bbr.lta lta_convert --inlta /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dmri/xfms/diff2anatorig.bbr.lta --invert --outlta /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dmri/xfms/anatorig2diff.bbr.lta mri_convert /nfsd/biopetmri4/Users/CauzzoOPA/FS_RECON/subjOPAPD01/mri/aparc+aseg.mgz /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dlabel/anatorig/aparc+aseg.nii.gz mri_binarize --i /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dlabel/anatorig/aparc+aseg.nii.gz --min .5 --dilate 4 --erode 2 --o /nfsd/biopetmri4/Users/CauzzoOPA/prove/tracula/res/subjOPAPD01/dlabel/anatorig/aparc+aseg_mask.nii.gz ERROR: Could not find thalamic nuclei segmentation in /nfsd/biopetmri4/Users/CauzzoOPA/FS_RECON/subjOPAPD01/mri/ ERROR: Thalamic nuclei segmentation is strongly recommended to use ERROR: for tracts that terminate in or travel near the thalamus ERROR: If there is good reason not to use it, set usethalnuc = 0 ################################################ Simone Cauzzo

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Postdoc position at MGH: Brainstem neuroimaging in Alzheimer's disease
by Jacobs, Heidi I.,PHD 20 Jan '26

20 Jan '26

The Athinoula A. Martinos Center for Biomedical Imaging, located within the Department of Radiology at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) in Boston, Massachusetts, has an opening for a highly qualified postdoctoral individual to work with Dr. Heidi Jacobs. The Jacobs lab is focused on improving the early detection and early treatment of Alzheimer’s disease. The lab focuses on the neuromodulatory subcortical nuclei, in particular the locus coeruleus, using a variety of approaches, including 7T MRI, PET imaging, pupil measurements, physiological recording, blood-based markers, cognitive assessments and non-invasive vagus nerve stimulation. This project is focused on the functional balance between the brainstem and cortex in relation to pathological changes in preclinical Alzheimer’s disease. This project will require combining fMRI and PET-data from existing datasets with computational modeling approaches. The Jacobs Lab consists of a multidisciplinary team of two instructors, four postdocs, two PhD-students, two clinical research coordinators and one project manager. The work in this project will be performed at the Athinoula A. Martinos Center for Biomedical Imaging, Charlestown Navy Yard. The candidate will be part of ongoing collaborations and work in a stimulating and inspiring environment. Our research group values open communication, motivation, optimism, mutual respect, teamwork, and innovative thinking. Dr. Jacobs is highly committed to individualized mentoring to help trainees achieve the most out of their postdoctoral candidature and to move forward in their career. At a minimum, the training environment will include professional development, one-on-one meetings, group lab meetings, frequent seminars and journal clubs, opportunities to present their work at national and international scientific conferences (i.e. Human Amyloid Imaging, Alzheimer’s Association International Conference), collaborations with partners within and outside MGH, and manuscript preparation for publication in high-impact journals. In addition, Dr. Jacobs has a strong funding record and will strongly encourage and provide mentorship in grant applications. Requirements: Candidates should hold a Ph.D. in Cognitive Neuroscience, Computational Neuroscience, bio/medical physics, Neuroimaging, Psychology (Biological), or a related discipline. Strong analytical, quantitative, and programming skills, along with experience in complex fMRI modeling, are essential, as is the ability to relate neuroimaging findings within a pathobiological framework of neurodegenerative diseases. The candidate should be highly motivated, a strong communicator, possess internal drive to learn independently, but also be comfortable with working as part of a larger collaborative team. A real necessity is a passion for science, strong scientific writing and organizational skills, and a positive attitude. Experience in Alzheimer’s disease or aging research would be beneficial. Apply: The successful candidate will have joint appointments at MGH and HMS. If interested, please send your CV, letter describing interests, background, major achievements, skills, goals and contact information for three professional references. Please send application materials to Dr. Heidi Jacobs, Associate Professor of Radiology, at hjacobs(a)mgh.harvard.edu<mailto:hjacobs@mgh.harvard.edu> ___________________________________________ Heidi Jacobs, PhD Associate Professor of Radiology Massachusetts General Hospital | Harvard Medical School Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging 149 13th Street Charlestown, MA 02129 hjacobs(a)mgh.harvard.edu www.heidijacobs.org<http://www.heidijacobs.org> Learn about what we do and why: https://shorturl.at/fEFa8 [A blue and black logo Description automatically generated] [signature_3581815700] Social media: Linkedin: https://www.linkedin.com/in/heidijacobs/ Bluesky: https://bsky.app/profile/heidijacobslab.bsky.social [Please note: I might send an email out of office hours, at weekends or during holidays. This suits me – but doesn’t mean I expect you to do the same]

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Re: mri_cc segmentation fault: Possibly due to M5 silicon incompatibility?
by fsbuild 19 Jan '26

19 Jan '26

External Email - Use Caution I’m not sure where the output comes from listing Freesurfer 5.3.0 in your previous email.  The recon-log seems to indicate you are actually running 8.1.0. But I do not expect Freesurfer 5.3.0 Intel binaries to run under the Rosetta emulation environment on a silicon Mac.  Even if it does run, since the M5 Mac OS and CPU architecture are different, your floating point results for any subject would likely not match results from any previous runs on an Intel processor. Before setting up the Freesurfer environment, I would explicitly run the bash shell,  $ bash$ export FREESURFER_HOME=/Applications/freesurfer/8.1.0$ source $FREESURFER_HOME/SetUpFreeSurfer.sh I would then copy any subject data you want to process into a directory like your home ($HOME) where you do not need any special permission to write to (see below).  The idea is to not modify the Freesurfer distribution by placing your own subject data there. $ cd… you are now in your home directory denoted by $HOME ...$ mkdir subjects$ cd subjects…. copy in subject data you want to process .. $ export SUBJECTS_DIR=$HOME/subjects$ ls $SUBEJCTS_DIR… you should see your data … Processing T1 and/or large images may not work on the silicon Mac unless you have at least 32G of physical RAM on the machine.  Even then it may not work because changes to the recon-all pipeline commands include python code which may require more (virtual) RAM than the memory management can handle.   The recon-all log says 22G of RAM are in use and there 1.5G of RAM free.  I’m assuming you are not running any other apps that cache data in RAM, browsers, etc. A workaround for this is to tell recon-all to revert back to the previous version of some pipeline commands by setting the environment variable FS_V8_XOPTS=0 on the recon-all command line, $ export FS_V8_XOPTS=0 && recon-all -i T1.nii.gz -s Pt01 -maskbfs -all The downside to this is the recon-all command will take longer to finish. Finally, if you continue to run into errors, you could try downloading and installing a current development build from,https://secure-web.cisco.com/14KJLuygmcYT1tDR1pvEv7VcSpwbhj7rIiogbQnrS… Please keep in mind we do not recommend development builds for long term/ongoing work since they may be unstable. So to summarize ..1) try using the bash shell to run commands (and set SUBJECTS_DIR differently)2) see if a recon-all can complete using export FS_V8_XOPTS=0 && recon-all …3) if the above does not resolve your errors, try a more recent development build - R. On Jan 17, 2026, at 12:47, Ajay Peddada <ajay.peddada(a)gmail.com> wrote:

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Re: NextBrain atlas: Missing hippocampal subfields in FreeSurfer 8.1
by Iglesias Gonzalez, Juan E. 19 Jan '26

19 Jan '26

Thank for the comprehensive feedback, Luis! * ROIs: A lot of small structures were merged with others when building (and then further simplifying) the atlas, including (pro-)subicular labels. Sorry for the inconvenience. Even with histology, it can be tricky to reliably label some of these. I’m CCing our co-author Martina in case she can shed further light on this. * Thanks for detecting the bug. Trying to keep all the versions has led to rather messy code. We are in the process of reorganizing / refactoring the code and hope to have a clean version out soon (2-3 weeks). * The error with the missing atlas should be solved by now in the development version; apologies for the inconvenience. Again: thanks for you feedback and for your patience with our new software! /E -- Juan Eugenio Iglesias http://www.jeiglesias.com From: Luis Alberto Barreiro Araújo <pg54004(a)alunos.uminho.pt> Date: Saturday, January 17, 2026 at 14:11 To: Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Cc: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu>, Tiago Gil Rodrigues Oliveira <tiago(a)med.uminho.pt>, Francisco Almeida <franciscojcga(a)gmail.com> Subject: NextBrain atlas: Missing hippocampal subfields in FreeSurfer 8.1 External Email - Use Caution Dear Dr. Iglesias, I'm a researcher at the University of Minho - ICSV Institute, conducting research on hippocampal patterns in Alzheimer's disease. I've used NextBrain for detailed hippocampal and full segmentation on NACC dataset subjects. Issue: I noticed your NextBrain demo website shows hippocampal structures including: prosubiculum (uncal, rostral, caudal) presubiculum (rostral, caudal) indusium_griseum supracallosal_subiculum However, these structures don't appear in either atlas_simplified or atlas_full YAML configuration files in FreeSurfer 8.1. I've verified this by checking: data_simplified/atlas_names_and_labels.yaml data_full/atlas_names_and_labels.yaml Additionally, when attempting to use atlas_full, the segmentation crashes with "IndexError: list index out of range" at label 266, suggesting the data_full/combined_atlas_labels_1mm.yaml config is incomplete (maps only 265 of 334 labels). Questions: Are these additional hippocampal subfields available in FreeSurfer dev or a more recent atlas version? If not yet released, are they planned for a future update? Would you recommend an alternative approach for segmenting these specific structures? Should I post these issues in the official FreeSurfer GitHub repository for broader advice ? Note: I'm running NextBrain via FreeSurfer 8.1 Docker container, due to incompatibility issues in our workstation with the OS. The Docker image was missing both the atlas files and the Python segmentation scripts, so I had to manually download: * atlas_simplified.zip and atlas_full.zip from the FTP server * ERC_bayesian_segmentation scripts from the GitHub dev branch * SuperSynth_August_2025.pth model (1GB) After mounting these files into the container, atlas_simplified works perfectly. However, atlas_full crashes as described above, and neither atlas contains the additional hippocampal subfields visible in your demo. From my understanding, recently (in the past week) a new version with the bayesian segmentation folder was put available but the issues I have remain. Another small note: I had to manually correct the mri_histo_atlas_segment_fireants.sh script because some of the parameters for the python scripts where missing. I'm not sure if that's supposed to happen or if it's a version error. Thank you for your attention. I look forward to receiving a response. Best regards, Luís Researcher, Informatics Engineering University of Minho - ICVS

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NextBrain atlas: Missing hippocampal subfields in FreeSurfer 8.1
by Luis Alberto Barreiro Araújo 17 Jan '26

17 Jan '26

External Email - Use Caution Dear Dr. Iglesias, I'm a researcher at the University of Minho - ICSV Institute, conducting research on hippocampal patterns in Alzheimer's disease. I've used NextBrain for detailed hippocampal and full segmentation on NACC dataset subjects. Issue: I noticed your NextBrain demo website shows hippocampal structures including: prosubiculum (uncal, rostral, caudal) presubiculum (rostral, caudal) indusium_griseum supracallosal_subiculum However, these structures don't appear in either atlas_simplified or atlas_full YAML configuration files in FreeSurfer 8.1. I've verified this by checking: data_simplified/atlas_names_and_labels.yaml data_full/atlas_names_and_labels.yaml Additionally, when attempting to use atlas_full, the segmentation crashes with "IndexError: list index out of range" at label 266, suggesting the data_full/combined_atlas_labels_1mm.yaml config is incomplete (maps only 265 of 334 labels). Questions: Are these additional hippocampal subfields available in FreeSurfer dev or a more recent atlas version? If not yet released, are they planned for a future update? Would you recommend an alternative approach for segmenting these specific structures? Should I post these issues in the official FreeSurfer GitHub repository for broader advice ? Note: I'm running NextBrain via FreeSurfer 8.1 Docker container, due to incompatibility issues in our workstation with the OS. The Docker image was missing both the atlas files and the Python segmentation scripts, so I had to manually download: * atlas_simplified.zip and atlas_full.zip from the FTP server * ERC_bayesian_segmentation scripts from the GitHub dev branch * SuperSynth_August_2025.pth model (1GB) After mounting these files into the container, atlas_simplified works perfectly. However, atlas_full crashes as described above, and neither atlas contains the additional hippocampal subfields visible in your demo. From my understanding, recently (in the past week) a new version with the bayesian segmentation folder was put available but the issues I have remain. Another small note: I had to manually correct the mri_histo_atlas_segment_fireants.sh script because some of the parameters for the python scripts where missing. I'm not sure if that's supposed to happen or if it's a version error. Thank you for your attention. I look forward to receiving a response. Best regards, Luís Researcher, Informatics Engineering University of Minho - ICVS

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mri_cc segmentation fault: Possibly due to M5 silicon incompatibility?
by Ajay Peddada 17 Jan '26

17 Jan '26

External Email - Use Caution Hello FreeSurfer Developers, I am trying to run recon-all on a T1.nii file on my M5 macbook pro. I have set my environment variables per documentation instructions: export FREESURFER_HOME=/Applications/freesurfer/8.1.0 source $FREESURFER_HOME/SetUpFreeSurfer.sh export SUBJECTS_DIR=$FREESURFER_HOME/subjects export FS_LICENSE=$FREESURFER_HOME/license.txt I am concerned if the issue is due to me trying to run freesurfer on an M5 macbook. Also, I'm getting this recurring warning: if: Empty if. then: Command not found. 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: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Platform: MacOSX Tahoe 26.2 (25C56) 3) uname -a: Darwin Ajays-MBP.attlocal.net 25.2.0 Darwin Kernel Version 25.2.0: Tue Nov 18 21:09:49 PST 2025; root:xnu-12377.61.12~1/RELEASE_ARM64_T8142 arm64 4) recon-all.log: see attached

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freeview overlay_custom: how to create a transparent/“no overlay” band around 0 for diverging maps?
by Camilo Castelblanco Riveros 15 Jan '26

15 Jan '26

External Email - Use Caution Hello Freesurfer Community, I’m visualising a surface overlay in Freeview (fsaverage inflated surface) using custom JSON colourmaps. For sequential features (mean/std), this works fine, but for signed significance-like maps, I want a diverging display with a “dead zone” around 0 (e.g., do not colour values between -2 and +2, so the underlying sulc/curv grey shading remains visible). With built-in colourmaps, Freeview can effectively truncate the middle, but with overlay_custom, the overlay always paints a colour (no alpha/transparent option), so I can’t keep the native curvature shading in the middle range. *Example command*: freeview -f $SUBJECTS_DIR/fsaverage/surf/rh.inflated:annot=aparc.annot:annot_outline=1:overlay=/path/to/sig.mgh:overlay_custom="/path/to/custom.json" -viewport 3d -layout 1 *Question*: Is there a supported way in Freeview to make a value interval (e.g. [-2,2]) render as “no overlay/transparent” when using custom overlays, or is the intended workflow to pre-mask the overlay (e.g., set values in that interval to NaN) before loading? [image: image.png] Thank you! P.S. Is there a way to save images in vector format or PDF? The saving option hasn't allowed me =================================== *Camilo Castelblanco Riveros (He/His)* Neuroscience Ph.D. Candidate (G4) Robertson Lab <https://secure-web.cisco.com/11IId-FSIj2OB9o07kaQlCFuuH7EcJfRBMfniDZE2ADa-k…> & Bujarski Lab <https://secure-web.cisco.com/1dyd3QN20M10b3cHLFbP2mCJe0t7Zk0cwZJ25BnaffnKVn…> Student Interest Group in Neurology (SIGN <https://secure-web.cisco.com/1F4yBWY2i0PLHYagzW9cPA92DGKJvl4QglUz0VOM7rIVDd…>) Co-Leader Global Health Fellow e: ccastelblanco.gr(a)dartmouth.edu Zoom <https://secure-web.cisco.com/1TpnrTMiSXuR0AZwK-n65X5F9L-iGGIlwdoOm1tvaFTtsG…>

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Fwd: Clarification on FreeSurfer recon-all Output and Preprocessing Steps
by Akanksha Upadhyay 15 Jan '26

15 Jan '26

External Email - Use Caution ---------- Forwarded message --------- From: Akanksha Upadhyay <aupadhyay(a)cs.du.ac.in> Date: Sun, Dec 21, 2025 at 6:09 PM Subject: Clarification on FreeSurfer recon-all Output and Preprocessing Steps To: <freesurfer(a)nmr.mgh.harvard.edu> Dear FreeSurfer Support Team, Greetings of the day. I am attempting to replicate a previously published work and have applied the recon-all pipeline on our structural MRI data (T1w.nii) using FreeSurfer. After segmentation and normalization, the output we are obtaining appears unusual to us. I would like to confirm whether these results are expected or if additional preprocessing steps are required prior to running recon-all . I have also attempted reorientation of the input image; however, I was only able to find GUI-based orientation options. I would appreciate your guidance on the following points: 1. Whether the observed segmentation and normalization outputs are expected, or if further preprocessing steps (such as reorientation, intensity correction, or format conversion) should be performed before running recon-all. 2. If manual reorientation is recommended, how should the orientation be determined (e.g., reference axes, alignment criteria, or specific angles)? 3. Any best practices for preparing T1w.nii files to ensure optimal processing with FreeSurfer. I am attaching screenshots of the normalization and segmentation results (aseg output) for your reference. Kindly guide me on how to proceed further. Thank you very much for your time and support.

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Re: SynthSR - White Block Issue in the Processed T1 image
by fsbuild 13 Jan '26

13 Jan '26

External Email - Use Caution Wondering now what version of MacOS you are running.  While Freesurfer 8.1.0 was not tested on MacOS Tahoe (26.X), we’ve noticed that some mri_synth* commands did not always work correctly on the older MacOS Monterey (12.X) and Ventura (13.X) systems.  At least for FS 8.1.0, we saw some of those commands run more successfully on macOS Sonoma (14.X) and Sequoia (15.X), presumably from bug fixes and updates, including GPU performance.  Please let us know if you find the output is markedly different on Linux compared to (a specific version of) MacOS. - R. On Jan 13, 2026, at 00:09, Tejendra Singh <tejendra.singh.cp(a)gmail.com> wrote:        External Email - Use Caution        Thank you for the suggestion. To clarify, the white block artefacts are present in the saved SynthSR NIfTI output itself, not just during visualization. I observe the same rectangular regions when opening the output in multiple viewers (e.g., Freeview, MRIcron), and they persist after reloading the file.For context, I am running: OS: macOS (Apple Silicon); System: MacBook Air (M-4); FreeSurfer: 8.1.0 (arm64 build); Graphics: Integrated Apple GPU; SynthSR command: mri_synthsr (default model and also tested with --lowfield). I will try re-running one of the affected subjects on a different system (Linux workstation) and compare the SynthSR output to see if the artefact reproduces. I will report back once I have tested this.Thanks again for the helpful suggestion. On Mon, Jan 12, 2026 at 1:35 PM fsbuild <fsbuild(a)contbay.com> wrote:         External Email - Use Caution        I’m wondering if this is a graphics issue causing the screen not to update properly, related to the fact that you are using T1 images.  You could try one of the subjects that displays the erroneous output on a different system and see if you get the same result.  Maybe you could let us know what the system is you are running on including the OS and what your graphics hardware is.  - R. On Jan 12, 2026, at 00:57, Tejendra Singh <tejendra..singh.cp@gmail..com> wrote:         External Email - Use Caution         This is the issueOn Mon, Jan 12, 2026 at 11:25 AM Tejendra Singh <tejendra.singh.cp(a)gmail.com> wrote: Hello everyone, I am using SynthSR (FreeSurfer 8.1.0, mri_synthsr) to standardize T1-weighted MRI scans across a multi-protocol clinical dataset. The majority of subjects process correctly; however, for a small subset of scans, the SynthSR output contains prominent white rectangular/block artefacts over the brain volume.Key observations: The artefacts are not present in the original T1 imagesThey appear only in the SynthSR outputThe affected original scans are already 1 × 1 × 1 mm isotropicOriginal images otherwise appear visually normal (no obvious truncation or corruption)Artefacts look axis-aligned (rectangular slabs), suggesting a reconstruction failure rather than anatomyExample workflow:mri_synthsr \   --i sub-XX_T1w.nii \   --o sub-XX_synthsr.nii.gzQuestions: Are these white block artefacts a known failure mode of SynthSR for certain inputs?Are there recommended preprocessing checks (e.g., header/orientation fixes) to reduce this issue?Would trying the --v1 model be advisable in such cases?If the original scan is already clean and isotropic, is it methodologically acceptable to exclude SynthSR output and retain the original image for downstream processing?I am currently treating SynthSR as an exploratory preprocessing step and excluding affected subjects from the SynthSR-based pipeline, but I would appreciate guidance on best practices.Thank you for any insights  <Screenshot 2026-01-12 at 11.26.45 AM.png>_______________________________________________Freesurfer mailing list -- freesurfer(a)nmr.mgh.harvard.eduTo unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/ _______________________________________________ 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/1mpI2pDlMT7dsUzFPkVklGSe5u0LlWDd2br91FPaYO6NZG… 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/1u4Q66NudVvgBCN5_TnfNHEjisLGf3rtd-0sBX… . _______________________________________________ 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/1mpI2pDlMT7dsUzFPkVklGSe5u0LlWDd2br91FPaYO6NZG…

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