Freesurfer

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30055 discussions

Problem with applying FreeSurfer EasyAtlas warp format
by Chen, Yuqian 04 Dec '25

04 Dec '25

Dear FreeSurfer users, I’m attempting to use mri_warp_convert to convert an EasyAtlas transform into ITK format, but the resulting transform is incorrect when applied or visualized in 3D Slicer (see image below). The deformation field shrinks the brain, suggesting a possible scaling issue in the converted transform. Here is the command line I used: mri_warp_convert --inras sub-05_brain_warp.nii.gz --outitk sub-05_brain_warp-itk.nii.gz -g sub-05_brain.nii.gz<http://.nii.gz/> [Image] Has anyone encountered this behavior or knows whether additional steps are needed when converting EasyAtlas transforms to ITK format? Thank you for any guidance. Regards, Yuqian Chen, Ph.D. Postdoctoral Research Fellow, Harvard Medical School 399 Revolution Drive, Suite 1180, Somerville, MA 02145 ychen128(a)bwh.harvard.edu<mailto:ychen128@bwh.harvard.edu>

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Recon-all with Brainmask Input
by Anna Crawford 03 Dec '25

03 Dec '25

External Email - Use Caution Hello, I had a question about re-running recon-all with a precalculated brainmask. I have a brain mask that was created outside of FreeSurfer that I would like to use instead of the brainmask that is created in recon-all. I tried the following command (also with the mask in its original .nii form) and I get an error that the brainmask doesn't exist and thus does not continue throughout the pipeline (attached). recon-all -subjid test -i sub-HV3WJK_ses-MRI_rec-t1_N4norm.nii -xmask tweakedFSBrainMask2.mgz -all -noskullstrip error: mghRead(/home/acrawford/ATP_calibration_data/sub-HV3WJK/ses-MRI/run-001/fsNormPipeline_1/FStweakedMask/mri/brainmask.mgz, -1): could not open file\00 error: mri_em_register: could not open mask volume brainmask.mgz. \00 I have also tried running the full recon-all as is, then substituting in my brainmask and the skull-stripped T1 (brain.mgz) using the -autorecon2 -autorecon3 flags, but continue to run into errors. Additionally, I tried just using the skull-stripped T1 as the input file to recon-all -all which also did not work. Is there a way to run recon-all with an 'outside' mask? Thank you, Anna _________________________ Anna Crawford Senior Image Analyst Phone: +1 (475) 318-8228 https://secure-web.cisco.com/1xGC1sEawWmlv8GxcdUL2zP-fxq-1FmQXHLPVcKBZRMk30…<https://secure-web.cisco.com/1VLzeHvfaohhAFcoPLU3_Ow60GssgJipCmxB89BVY9HZda…> [cid:84668487-aed4-4dc5-8b0f-b61383239667] CONFIDENTIALITY NOTICE: Proprietary/Confidential Information belonging to XingImaging, LLC and its affiliates may be contained in this message. If you are not a recipient indicated or intended in this message (or responsible for delivery of this message to such person), or you think for any reason that this message may have been addressed to you in error, you may not use or copy or deliver this message to anyone else. In such case, you should destroy this message and are asked to notify the sender by reply e-mail.

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Re: Flatmap Coordinates Distance
by Glasser, Matthew 01 Dec '25

01 Dec '25

External Email - Use Caution We have tools in Connectome Workbench to compute geodesic distances accurately on the midthickness surface. If you have the same mesh topology between the flat map and a midthickness, you can just select the same vertices. Matt. From: "Fischl, Bruce R.,PHD" <BFISCHL(a)mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, December 1, 2025 at 10:01 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Re: Flatmap Coordinates Distance Hi Tom Distances in the flat map should be in mm and within 10-15% of geodesics in the cortex. You could also use great circles on the sphere, which should give you about the same error percent, but you would need to scale the sphere so it has the same surface area as the cortex I believe Cheers Bruce From: Possidente, Thomas <tposside(a)bu.edu> Sent: Monday, December 1, 2025 9:53 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Flatmap Coordinates Distance External Email - Use Caution Hi there, I have flattened a patch from fsaverage surface using mris_flatten and I would like to find the distance between two points on the flatmap. I believe that simply calculating the distance between coordinate points on the flatmap would not be interpretable because the units are no longer in millimeters (due to distortions during flattening). Please let me know if this is correct. I have found that I can map the vertex indices back into RAS 3D space and get the distance between 2 vertices that way, but because of cortical folding, it is different from the distance along the cortex between the two points. Is there any way to get the distance along the cortex between 2 vertices in interpretable units (ex. millimeters)? I am using Freesurfer 7.4.1 and Matlab 2023a to read in the any surface/patch/label files. Thank you for all the great work that you do! Best, Tom Thomas (Tom) Possidente | He/Him Doctoral Candidate | Boston University Brain, Behavior, & Cognition | Somers Lab ________________________________ 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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Flatmap Coordinates Distance
by Possidente, Thomas 01 Dec '25

01 Dec '25

External Email - Use Caution Hi there, I have flattened a patch from fsaverage surface using mris_flatten and I would like to find the distance between two points on the flatmap. I believe that simply calculating the distance between coordinate points on the flatmap would not be interpretable because the units are no longer in millimeters (due to distortions during flattening). Please let me know if this is correct. I have found that I can map the vertex indices back into RAS 3D space and get the distance between 2 vertices that way, but because of cortical folding, it is different from the distance along the cortex between the two points. Is there any way to get the distance along the cortex between 2 vertices in interpretable units (ex. millimeters)? I am using Freesurfer 7.4.1 and Matlab 2023a to read in the any surface/patch/label files. Thank you for all the great work that you do! Best, Tom Thomas (Tom) Possidente | He/Him Doctoral Candidate | Boston University Brain, Behavior, & Cognition | Somers Lab

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Re: FreeSurfer License Key
by fsbuild 30 Nov '25

30 Nov '25

External Email - Use Caution  Please fill out the form at the URL listed below, and provide an email address where the license can be sent to you,https://secure-web.cisco.com/1oyFRTZrSHzcLBVKUWFPUQyoipUrNqfBLPB2s-4CDJ… On Nov 30, 2025, at 16:25, Batuhan Sönmez <batuhan.snmz5759(a)gmail.com> wrote:        External Email - Use Caution         _______________________________________________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/

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FreeSurfer License Key
by Batuhan Sönmez 30 Nov '25

30 Nov '25

External Email - Use Caution

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TumorSynth
by Cogno, Nicolo 26 Nov '25

26 Nov '25

Hi, I’ve just found out about TumorSynth on this webpage https://surfer.nmr.mgh.harvard.edu/fswiki/TumorSynth. I’ve installed FreeSurfer 8.1.0 and wanted to try it out, but the command doesn't exist. However, the webpage says that it should be available on FS v7.4.0 onwards. How should I proceed? I would like to try the multi-sequence input support. Thank you very much, Nicolò ------------------------------------------------------------------------------ Nicolò Cogno, Ph.D. Postdoctoral fellow in Radiation Oncology Massachusetts General Hospital / Harvard Medical School

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T1 + DTI for thalamus segmentation Tensorflow version
by Jörg Stadler 26 Nov '25

26 Nov '25

External Email - Use Caution Hi, I try to run the https://secure-web.cisco.com/1OB24sXJsXKpFV3_YZf2OoUc5HIGSgT5Os8CiD0Kw5KeUJ… code, but I got stuck. I created a conda env with tensorflow 2.20, this gives me a ValueError: Unrecognized keyword arguments passed to BatchNormalization: {'fused': False} Same with tensorflow 2.16. It seems, that the 'fused' parameter was removed after version 2.4. Tensorflow 2.4 was available under python 3.6, but with conda create -n freesurfer python=3.6 and pip install tensorflow==2.4.0 I can only install versions from 2.16 onwards. Version 2.4 is not available. Removing the {'fused': False} gives me an error at input_shape = last_tensor.shape.as_list()[1:] ^^^^^^^^^^^^^^^^^ AttributeError: 'list' object has no attribute 'shape' How can I solve this dependency problem? Jörg

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Using the Glasser Cortical Atlas
by Carly McIntyre-Wood 25 Nov '25

25 Nov '25

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FreeSurfer 8.X Container?
by AmirHussein Abdolalizadeh 25 Nov '25

25 Nov '25

External Email - Use Caution Hi Freesurfer users/experts, I am looking for a containerized version of FreeSurfer 8.X. If none is available, please let me know if there are any plans to release it as a containerized version. Many people use high-performance clusters for their FreeSurfer analysis, which makes the recent FreeSurfer a bit not HPC-user-friendly; for example, the new recon-all requires 80GB RAM, so it must run on an HPC, but switching to the "cuda" version of some Python commands requires sudo - which is not often given to the HPC users. Best, Amir

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