Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30127 discussions

License Not Received After Registration — FreeSurfer 8.2.0 / Ubuntu 24.04
by yilunshi2004 18 Sep '26

18 Sep '26

External Email - Use Caution Hello FreeSurfer team, I registered for a FreeSurfer license using this email address. I received the mailing-list confirmation and welcome messages, but no license.txt or license text. I also checked spam. Could you please check whether my license registration was completed and resend the license? If it was not completed, please help me resolve the registration issue. I plan to use FreeSurfer 8.2.0 on Ubuntu 24.04 for academic MRI research. Thank you.

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(无主题)
by cz1394004851＠163.com 18 Sep '26

18 Sep '26

External Email - Use Caution 你好能不能检查一下，为什么很多申请邮件都发到我这里

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FreeSurfer license not received after registration
by Chensj 18 Sep '26

18 Sep '26

External Email - Use Caution Hello FreeSurfer team, I registered for a FreeSurfer license using this email address. I received the mailing-list confirmation and welcome messages, but no license.txt or license text. I also checked spam. Could you please check whether my license registration was completed and resend the license? If it was not completed, please help me resolve the registration issue. I plan to use FreeSurfer 7.4.1 on Ubuntu 22.04 for academic MRI research. Thank you.

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FreeSurfer license not received after registration
by Chensj 18 Sep '26

18 Sep '26

External Email - Use Caution Dear FreeSurfer team, I submitted the FreeSurfer license registration using the email address from which I am sending this message. I have received the GNU Mailman confirmation and the Freesurfer mailing-list welcome message, but no license.txt file or license text. I have checked my inbox and spam folder. Could you please resend my license, or advise how to complete license issuance? I plan to run FreeSurfer 7.4.1 on Ubuntu 22.04 / Linux Intel for academic MRI research. Thank you for your help.

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License.txt not received after registration (live outside US)
by 李亚锋 18 Sep '26

18 Sep '26

External Email - Use Caution Dear FreeSurfer team, I registered for a FreeSurfer license key via the registration page on 2026-09-17, using the email address liyafengna(a)foxmail.com. I have subscribed to and confirmed the freesurfer mailing list successfully (I received the confirmation and welcome messages), but I have not received any email containing the license.txt file. I have checked both my inbox and spam folder. Could you please advise whether the license email can be resent to a different address? I can provide an alternative address (e.g. a Gmail account) if delivery to the current domain is blocked. Registration details: Name: Yafeng Li Institution: Shenzhen University Country: China Platform: Linux/Intel Thank you very much. Best regards, Yafeng Li

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lack of cerebellum in freesurfer clinical
by Aimee Flores 10 Sep '26

10 Sep '26

External Email - Use Caution Dear freesurfer team, I am running the freesurfer clinical and we found that it does not extract the cerebellum by design. However, for coregistering the t1 to other imaging modalities it would be important to have a whole brain mask. I wonder if there is any solution for this. Best wishes, Aimee Flores -- PhD candidate at Charité – Universitätsmedizin Berlin Neurology Department. Max Planck Institute for Human Cognitive and Brain Sciences. Stephanstrasse 1a, 04103 Leipzig, Germany. Tel: +49(0)3419940-2256 Neurotech Stroke project Instagram: https://secure-web.cisco.com/19oI9BK5igUPkhRSoXPEfneexkjWlRWfv0N0paLp_Caws-… X: https://secure-web.cisco.com/1ZGkNThsM86iaEcfI1-ga8G_72WN0Ve518MR_ojtBII6jh… LinkedIn: http://secure-web.cisco.com/1TjxqTx_gQ9JRdOa14ckrvdeMhX5xdy2MqNOBlVgvzH_kgp… YouTube: https://secure-web.cisco.com/1d6ZS7_sRE3xPAYpp6ozaS6svy1FpF4rRnneu_CBmfoJxp… Website: https://secure-web.cisco.com/1g_n3ZldRmGbDnDtQUnSDsiQtXnPhjges8BccTPyFMKRug…

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FreeSurfer license registration – repeated 504 Gateway Timeout
by masahiro.joko＠fujita-hu.ac.jp 10 Sep '26

10 Sep '26

External Email - Use Caution Dear FreeSurfer Support Team, I am trying to obtain a FreeSurfer license.txt file for non-profit acade mic research, but the registration form repeatedly returns a “504 Gatew ay Timeout” after submission. I have tried the registration form multiple times, but no license email has arrived. Name: Masahiro Joko Institution: Fujita Health University, Japan Intended use: Non-profit academic research Operating system: Linux / Ubuntu 24.04 on WSL2 FreeSurfer version: 8.2.0 Could you please advise how I can obtain the license.txt file, or issue one manually if possible? Thank you very much for your assistance. Best regards, Masahiro Joko

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mri_gtmpvc error: segmentation ROIs disappear in PET space
by Qassim Alkassir 08 Sep '26

08 Sep '26

External Email - Use Caution Hello, I am using PETSurfer/mri_gtmpvc for PET quantification in the WRAP Alzheimer's cohort. I am encountering a reproducible error when regions present in gtmseg.mgz have no voxels after the segmentation is mapped into PET space. I searched the mailing-list archives and found a previous discussion of the same error message involving segid 29. In our data, however, the affected labels differ between subjects, so I wanted to ask what the recommended general approach is. What I am trying to accomplish ------------------------------ We are processing motion-corrected, frame-averaged 11C-PiB PET images with PETSurfer. Our PET images are approximately: Matrix: 128 x 128 x 63 Voxel size: 2.574 x 2.574 x 2.425 mm Voxel volume: 16.07 mm^3 The corresponding gtmseg.mgz images have: Voxel size: 0.5 x 0.5 x 0.5 mm Voxel volume: 0.125 mm^3 Command ------- The relevant mri_gtmpvc options generated by our PETSurfer workflow are: mri_gtmpvc \ --psf 0 \ --no-tfe \ --seg gtmseg.mgz \ --default-seg-merge \ --auto-mask 10 0.01 \ --mgx 0.01 \ --no-reduce-fov \ --no-rescale \ --save-input \ ... I have attached the full PETSurfer log from a representative failed subject. It contains the complete generated command and output. Exact error ----------- For example: ERROR: creating region for nthseg=22, segid=78, Left-WM-hypointensities It may be that there are no voxels for this seg when mapped into the input space. I initially encountered this problem in another subject for segid 79 (Right-WM-hypointensities). Before changing the segmentation or adding replacement rules, I tested four additional independent PiB subjects using the same unmodified workflow. gtmseg completed successfully for all four subjects. PETSurfer completed successfully for one subject and failed during mri_gtmpvc for three subjects. Results ------- The regions producing mri_gtmpvc errors were: Subject SegID Region GTM vol PET vox ---------------------------------------------------------------- WRAP1 78 Left-WM-hypointensities 6 mm^3 0 WRAP1 79 Right-WM-hypointensities 5 mm^3 0 WRAP2 31 Left-choroid-plexus 6 mm^3 0 WRAP2 78 Left-WM-hypointensities 21 mm^3 0 WRAP2 79 Right-WM-hypointensities 1 mm^3 0 WRAP3 78 Left-WM-hypointensities 2 mm^3 0 We also have an informative within-subject comparison in WRAP3: segid 78: GTM volume = 2 mm^3 PET-space representation = 0 voxels mri_gtmpvc reports an error for segid 78 segid 79: GTM volume = 46 mm^3 PET-space representation = 1 voxel mri_gtmpvc does not report an error for segid 79 For the failing labels, we directly counted the voxels in both gtmseg.mgz and the PET-space segmentation at: no_pvc_6.0fwhm/aux/seg.nii.gz In every case listed above, the label is present in gtmseg.mgz but has zero voxels in the PET-space segmentation. This makes us suspect that the immediate failure occurs when a region retained in the GTM definition receives no voxel representation after mapping the segmentation onto the much coarser PET grid. One detail that of note was that total region volume alone does not determine whether a label survives. For example, segid 78 in WRAP2 occupies 21 mm^3 in gtmseg.mgz, which is greater than the volume of one PET voxel (16.07 mm^3), but it still maps to zero PET voxels. Questions --------- 1. What is the recommended PETSurfer/mri_gtmpvc approach when a valid region in gtmseg.mgz has zero voxels after mapping into PET space? 2. For segids 78 and 79 (Left/Right-WM-hypointensities), is --merge-hypos intended for this situation? 3. We also see the same problem for segid 31 (Left-choroid-plexus). Should choroid plexus be merged/replaced for GTM analysis, or should this be handled differently? 4. More generally, should very small regions be merged before GTM construction, or is there another recommended way to handle regions that disappear at PET resolution? Additional FreeSurfer context ----------------------------- The anatomical FreeSurfer reconstructions were originally generated with FreeSurfer 8. The PETSurfer/gtmseg environment currently uses FreeSurfer 7.4.0. Because the FreeSurfer 8 reconstructions did not contain the classical talairach.m3z expected by the FreeSurfer 7.4 gtmseg, we generated talairach.m3z using FreeSurfer 7.4 mri_ca_register. gtmseg subsequently completes successfully for all subjects tested. The error described above occurs later during mri_gtmpvc. 1) FreeSurfer version: freesurfer-linux-ubuntu20_x86_64-7.4.0-20230510-e558e6e 2) Platform: Ubuntu Linux, x86_64 3) uname -a: Linux hpclogin.sri.utoronto.ca 5.4.0-132-generic #148-Ubuntu SMP Mon Oct 17 16:02:06 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux 4) PETSurfer log: See attached. I have attached the PETSurfer log from WRAP2, which demonstrates the failure for three different labels (31, 78, and 79). Thank you, Qassim Alkassir

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WM segmentation in tutorial Subj001
by Bélinda Boudi 08 Sep '26

08 Sep '26

External Email - Use Caution Hello Freesurfer team, I am working through the Freesurfer tutorial using the "Subj001" dataset. I ran recon-all using Freesurfer 8.2.0 on macOS. While looking through wm.mgz I noticed what appears to be a small region of white matter in an unusual location that is also included within the pial surface (see the attached pictures). Interestingly, it also does not appear in brainmask.mgz. I was wondering if you could help me understand what this represents and if it is something I should address. If it does need to be corrected, I am unsure which volume I should edit. I thought of deleting the relevant voxels from wm.mgz, but I would be concerned about affecting the surface reconstruction. I was wondering what you would recommend as the appropriate way to correct this, if any correction is needed. Thank you for your help. Best, Belinda Boudi

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Extract additional scalar metrics along reconstructed white matter pathways
by Durgerian, Sally 07 Sep '26

07 Sep '26

External Email - Use Caution Hello, I have run TRACULA on a group of subjects, and have text output for standard DTI metrics. I would like to see what difference it makes to do free water correction on the data by evaluating the FWC metrics along the same paths created in TRACULA. A google search of this question suggested that there is an extscalar option in TRACULA that I can use, but I don't see it in any of the documentation. Am I being led down the garden path by AI, or is this a thing? If so, how do I use it? Thanks, Sally [cid:37544fa9-a649-4fc9-a44c-85d8e5f0c3de] Sally Durgerian Senior Research Engineer | Division Of Radiology Cleveland Clinic | 9500 Euclid Ave. | Cleveland, OH 44195 (414) 364-7091 | DURGERS(a)ccf.org Please consider the environment before printing this e-mail Cleveland Clinic is a nonprofit, multispecialty academic medical center that's recognized in the U.S. and throughout the world for its expertise and care. Visit us online at http://secure-web.cisco.com/1Y0P0wokYL5ZNdbMxGt9sslPpjXazl-6TTCS2mNWS3v6z3q… for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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