Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30128 discussions

Hippocampal segmentation
by Tricia Merkley 18 Oct '25

18 Oct '25

External Email - Use Caution Hello FreeSurfers, In visually reviewing the output of the hippocampal subfield segmentation, there are a few subjects that show gaps in the segmentation. For some, this may be due to variation in intensities in the region, but for others we are unable to tell why this may happen. Some also appear to include more than the hippocampus in the boundaries. Please see the attached examples. This was run with FS version freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b Any idea why this may happen? Should we be concerned about the validity of the segmentation, or does it accurately represent the neuroanatomy for these individuals (normal variation vs. pathology)?

3 2

Re: Inquiry About Commercial FreeSurfer License
by fsbuild 17 Oct '25

17 Oct '25

External Email - Use Caution There have been various inquiries about a “commercial” license over the years.  If you search the mail list archive,https://secure-web.cisco.com/1ehbU0ZdrxTr8caxjZMTfGmHMyGzs7ZOr-cmBJ… - for a term like “commercial”, you will see a recent posting from 2025,https://secure-web.cisco.com/1rnH-cq1_4rdGD8oUshS-WLrPJ0SCcLdV3U15wxCZ… - pointing out that while the freesurfer source code available on GitHub is essentially open source per the terms of the MGH license, the freesurfer distribution is also subject to any restrictions listed in the licenses of the 3rd party software it utilizes.  Those 3rd party licenses and/or copyrights are reproduced in the distribution, and may require negotiating a paid for license with individual 3rd party vendors in order to use freesurfer in a commercial application or setting.  Once you decide upon a release of freesurfer to use, it is up to your organization to read thru the licenses, copyrights, etc. in that release and comply with any terms listed for commercial use. - R. On Oct 17, 2025, at 09:28, amira(a)multiwave.fr wrote:        External Email - Use Caution        Dear FreeSurfer Licensing Team,I am writing on behalf of Multiwave Technologies, a company engaged in research and development of Ultra low field MRI-related technologies. We are considering the integration of FreeSurfer within our internal workflows for neuroimaging analysis in the context of product development intended for clinical and commercial applications.To ensure full compliance with the FreeSurfer Software License Agreement, we would like to obtain further information regarding the commercial licensing options available. Specifically, we would appreciate details on:The applicable terms and conditions for commercial or industrial useThe licensing process and any required documentationAssociated fees or royalty structures, if applicableThank you for your time and assistance. We look forward to your guidance on the appropriate next steps to establish a commercial license.Kind regards,Amira TRABELSI BERGÉ-LAVAL | Head of OperationsMultiwave Technologieswww.multiwave.chHôtel Technoptic – CS 800012, rue Marc Donadille, 13 453 Marseille Cx 13 | FRANCE+33 (0) 4 13 42 15 25+33 (0) 6 17 55 77 76_______________________________________________ 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/1NCkKPdDfQoba6pvh59or4-Sj0FtrCZUIzMOg3weGgdLxv…

1 0

Raw Cortical Thickness Oscillations/Periodicity
by Jonathan P Dyke 17 Oct '25

17 Oct '25

External Email - Use Caution Hi. We have a question about the raw cortical thickness (CT) data exported from FS with read_curv. As an example, I loaded in the "bert" sample dataset, read the left hand cortical thicknesses and then dumped to a text file (attached). This comes straight from the FS Wiki (https://secure-web.cisco.com/1Elo3ZMPGo-51f9D5Cyve8XA0n_Ps0RopebqcC90a3MK_G…<https://secure-web.cisco.com/1xTVjn_11mS7O8kpk-Z_1qWqdnYVJGSS8DDdmA7uqHC1a7…>) Q. How can I make a histogram of cortical thickness? A: In Matlab you can use the read_curv() function, as in the example below. 1. thick = read_curv ('/usr/local/freesurfer/subjects/bert/surfer/lh.thickness'); hist (thick,100); Notice that there are many zero values that refer to areas where there's no cortical surface. The best procedure is to create a new array without the zero values and then make the histogram. The matlab code are just in these three lines. thick = read_curv(bert); fileID2 = fopen(outfile,'w'); fprintf(fileID2,'%s \n',thick); The first image below shows the first 500 thicknesses in the array while the second image shows the first 5,000. There is a distinct oscillation/periodicity in the data that is written out. We were wondering if this has to do with the way that FS rasters across the brain going from sulci to gyri, etc? If the data is placed in a histogram, in a normal control subject we do get and expect a Gaussian distribution. Please let us know! Thanks, Jon [cid:image001.png@01DC39D7.80AD5FB0] [cid:image002.png@01DC39D7.80AD5FB0] Jonathan P. Dyke, Ph.D., DABMP (MRI) Professor of Physics Research in Radiology Weill Cornell Medicine Citigroup Biomedical Imaging Center 516 East 72nd Street, New York, NY 10021 T: (212) 746-5781 jpd2001(a)med.cornell.edu<mailto:jpd2001@med.cornell.edu> https://secure-web.cisco.com/1xDwlFgVAFQAzueuGuiIfi8H88omfglOhOccGNEhiRaKVf…<https://secure-web.cisco.com/1Lnkj1qw7ihDOCfmxSKCVFoSzRb4AchVJ4tZveXJcU8yLE…> https://secure-web.cisco.com/1EOTpPLywEDR2CuhUClJfK5t2brb_dDumAmiW88_3zIzTi…<https://secure-web.cisco.com/1Vk4ZlA8td_XcHqE_xIWYF3DPPZztt5RTvnCLZOXo3Xbv-…> https://secure-web.cisco.com/18GxDz4dUCXj5gwG2zf-KrN73Zqbfpz-QRdv-qXAPlh1lY…<https://secure-web.cisco.com/11foGvXt-9ehohguhfB8iiX-faywHX81Sf7kmgUKGn3FBA…>

1 0

Validation of the thalamic nuclei segmentation
by Melissa Thalhammer 17 Oct '25

17 Oct '25

External Email - Use Caution Dear FreeSurfers, I read that criticism about the thalamic nuclei segmentation based on T1-images was raised (DOI: 10.1016/j.neuroimage.2022.119340<https://secure-web.cisco.com/1V8gZgz38WZjYs0sX-xsLC9vnYMqApMNA_X1Jr2Efj69f_…> and DOI: 10.1162/imag_a_00166<https://secure-web.cisco.com/1HuYBMxn8grUwviyS1dIybnKr9s2bpABgLeHoaKYUZXVIt…>) as overlaps with the Morel stereotactic atlas were not always satisfying. However, I was wondering whether the segmentations with the Morel atlas (registered to MNI space) of individual thalami can be considered a proper validation since individual variation of thalamic nuclei sizes are not taken into account and the atlas is not probabilistic. Can someone elaborate on this criticism? Thank you, Melissa

2 1

Northwestern PhD Program in Medical Imaging Now Open
by Amber Leaver 17 Oct '25

17 Oct '25

External Email - Use Caution The new HSIP Medical Imaging PhD Program at Northwestern University is now accepting applications through December 1st 2025. Applicants with backgrounds in imaging research and engineering are encouraged to apply. Accepted students will be trained by leaders in neuroimaging, cardiac MRI, and AI research. Details are here: https://secure-web.cisco.com/1HUnqC9KWE-hzipxDumpjrfgXUaFjTaPYlyYtxwZm8R1JQ… Don't hesitate to reach out with questions (and apologies for cross-posting). -- Amber Leaver PhD Track Leader, HSIP Medical Imaging Research Associate Professor of Radiology Feinberg School of Medicine Northwestern University

1 0

Inquiry About Commercial FreeSurfer License
by amira＠multiwave.fr 17 Oct '25

17 Oct '25

External Email - Use Caution Dear FreeSurfer Licensing Team, I am writing on behalf of Multiwave Technologies, a company engaged in research and development of Ultra low field MRI-related technologies. We are considering the integration of FreeSurfer within our internal workflows for neuroimaging analysis in the context of product development intended for clinical and commercial applications. To ensure full compliance with the FreeSurfer Software License Agreement, we would like to obtain further information regarding the commercial licensing options available. Specifically, we would appreciate details on: - The applicable terms and conditions for commercial or industrial use - The licensing process and any required documentation - Associated fees or royalty structures, if applicable Thank you for your time and assistance. We look forward to your guidance on the appropriate next steps to establish a commercial license. Kind regards, AmiraTRABELSI BERGÉ-LAVAL| Head of Operations Multiwave Technologies [http://secure-web.cisco.com/1x0Dsk_L1wqimzs-bW151XhMRHChHTnlsx88NdvryaUkx0v… Hôtel Technoptic – CS 80001 2, rue Marc Donadille, 13 453 Marseille Cx 13 |FRANCE +33 (0) 4 13 42 15 25 +33 (0) 6 17 55 77 76

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Re: SuperSynth installation
by fsbuild 16 Oct '25

16 Oct '25

External Email - Use Caution  Could you let us know what version of Ubuntu to you are going to upgrade to ? - R. On Oct 16, 2025, at 17:10, Iglesias Gonzalez, Juan E. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> wrote:Iglesias Gonzalez, Juan E. reacted to your message:From: Villagran Asiares, Alberto Gaston <Alberto.Villagran(a)med.uni-muenchen.de> Sent: Thursday, October 16, 2025 8:15:07 AM To: Freesurfer support list <freesurfer@nmr.mgh..harvard.edu> Subject: [Freesurfer] Re: SuperSynth installation         External Email - Use Caution        Dear Eugenio,Thanks for the info. I see I will have to update my ubuntu hahBest,Alberto Alberto Villagran, MSc.Medical imaging scientist, cBrainLMU University HospitalcBRAIN | Child Brain Research and Imaging in NeuroscienceDepartment of Child and Adolescent Psychiatry, Psychosomatics, and PsychotherapyCampus Innenstadt | Nussbaumstr. 5 | 80336 Munich, Germanyalberto.villagran@med.uni-muenchen.de | http://secure-web.cisco.com/1nGSvDspZWxdgPR1sZA1Ddu8OP8fRv7QkOPre5c9lSUtBNNcolbJJWn6dnifFYmaeaMKe4RcLRCVnjKDSnsjBNWaCl4WLIds_lPlIKQX13EWubOOIus0us8yUjevu-y-g0Ur0MdKqVIvOqIFE3x5XgBxHgONMKRa_OzIMfgbdi3uMEOPU1hLj205t7i6b9Qt9qY8FHEGXzAJHz66ksirse1AtYYyr5DIyDTORuE-LYpvd_3pBkVG78qUhT8zaSN5BNqGhZZNQgppniENfdT-HT4vW8JWXs8VB_p4CyYHwdytPLHAf8furJtro440VFQLy/http%3A%2F%2Fwww.lmu-klinikum.de%26nbsp;| www.pediatric-neuroimaging.de <OutlookEmoji-16899286937473dc1cc35-0fc6-4041-94c1-e0a3c397027d.png> The LMU University Hospital Munich is an institution under Public Law From: Iglesias Gonzalez, Juan E.. <JIGLESIASGONZALEZ(a)mgh.harvard.edu> Sent: Friday, 10 October 2025 16:27:21 To: Freesurfer support list Subject: [Freesurfer] Re: SuperSynth installation Dear Alberto,Download and install the development version of FreeSurfer:https://secure-web.cisco.com/1yz2W8Kd1LBwZeppq619mfpAsNA1W3BUwki… will be in there.Cheers,/Eugenio --Juan Eugenio Iglesiashttp://http://secure-web.cisco.com/1_OHx56-hiog6u-73LlrL9mKWhTSirsk… Asiares, Alberto Gaston <Alberto.Villagran(a)med.uni-muenchen.de> Date: Friday, October 10, 2025 at 3:57 AM To: freesurfer@nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] SuperSynth installation         External Email - Use Caution        Dear FS team, I would like to download and install the new tool SuperSynth, but in the website https://secure-web.cisco.com/1AFgBsT9D-DioLe5CupDDL-kdbqUMdZlz… is not clear to me how to get it. Thanks in advance,Best,Alberto Alberto Villagran, MSc.Medical imaging scientist, cBrainLMU University HospitalcBRAIN | Child Brain Research and Imaging in NeuroscienceDepartment of Child and Adolescent Psychiatry, Psychosomatics, and PsychotherapyCampus Innenstadt | Nussbaumstr. 5 | 80336 Munich, Germanyalberto.villagran@med.uni-muenchen.de | http://secure-web.cisco.com/1nGSvDspZWxdgPR1sZA1Ddu8OP8fRv7QkOPre5c9lSUtBNNcolbJJWn6dnifFYmaeaMKe4RcLRCVnjKDSnsjBNWaCl4WLIds_lPlIKQX13EWubOOIus0us8yUjevu-y-g0Ur0MdKqVIvOqIFE3x5XgBxHgONMKRa_OzIMfgbdi3uMEOPU1hLj205t7i6b9Qt9qY8FHEGXzAJHz66ksirse1AtYYyr5DIyDTORuE-LYpvd_3pBkVG78qUhT8zaSN5BNqGhZZNQgppniENfdT-HT4vW8JWXs8VB_p4CyYHwdytPLHAf8furJtro440VFQLy/http%3A%2F%2Fwww.lmu-klinikum.de%26nbsp;| www.pediatric-neuroimaging.de <OutlookEmoji-16899286937474ad8d43c-801e-4475-97e4-fdaee805a3fa.png> The LMU University Hospital Munich is an institution under Public Law _______________________________________________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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recon-all fails with "Invalid FreeSurfer license key" when executed via Docker SDK but works interactively
by Óscar Peña-Nogales 16 Oct '25

16 Oct '25

External Email - Use Caution Hi all, I’m running recon-all inside a Docker container, but it fails with the following error when launched programmatically through an SDK: ERROR: Invalid FreeSurfer license key found in license file /usr/local/freesurfer/license.txt If you are outside the NMR-Martinos Center, go to http://secure-web.cisco.com/1caZqJPIIzERnX6myZfn7lHvJljbS0zsXzR6nmSo47CLhLQ… to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. The command used by the SDK looks like this: docker run -v /usr/local/lib/python3.10/dist-packages/xxxx/execution/communication.patch:/usr/local/lib/python3.11/dist-packages/xxxx/sdk/communication.py:ro \ --cap-drop=NET_RAW -dt --name analysis_1420668 --entrypoint /bin/bash \ --cpus=4 --memory=16384m \ europe-west3-docker.pkg.dev/xxxx/freesurfer_530:dev-1.0 \ /xxxx/entrypoint.sh --project 2289 --analysis 1420668 \ --token xxxx --url https://secure-web.cisco.com/1_ZG55biN3BILRStBLxIfao5TAMons8aRRsmdYirMJ90Ow… \ --tool-path tool:run However, when I start the container manually (e.g., docker run -it ... /bin/bash) and run recon-all inside it directly, the license is detected and validated correctly. So the license.txt file at /usr/local/freesurfer/license.txt itself appears to be valid. This suggests the issue is related to *how the container is executed by the SDK or entrypoint*, possibly involving the entrypoint script /xxx/entrypoint.sh altering the environment before recon-all starts. The Docker container has: Ubuntu 22.04 Python 3.11 Has anyone seen a similar issue where FreeSurfer fails to validate the license only when invoked non-interactively? Are there specific environment variables or checks that recon-all performs which might differ when running under /bin/bash -c or through an SDK wrapper? Any insights or debugging suggestions would be greatly appreciated. Thanks!

3 6

Hippocampal subfield segmentation
by Tricia Merkley 14 Oct '25

14 Oct '25

External Email - Use Caution Hello FreeSurfer Developers, We are visually reviewing the output of the hippocampal subfield segmentation, and there are a few subjects that show a gap in the segmentation. For some, this may be due to variation in intensities in the region, but for others we are unable to tell why this may happen. Please see the two attached examples, with and without the segmentation. This was run with FS v7.1.0. Any idea why this may happen? Should we be concerned about the accuracy of the segmentation, or does it accurately represent the neuroanatomy for these individuals (potentially normal variation vs. pathology)? Thanks, Tricia Merkley

1 0

Raw Cortical Thickness Oscillations/Periodicity
by Jonathan P Dyke 10 Oct '25

10 Oct '25

External Email - Use Caution Hi. We have a question about the raw cortical thickness (CT) data exported from FS with read_curv. As an example, I loaded in the "bert" sample dataset, read the left hand cortical thicknesses and then dumped to a text file (attached). This comes straight from the FS Wiki (https://secure-web.cisco.com/1xTVjn_11mS7O8kpk-Z_1qWqdnYVJGSS8DDdmA7uqHC1a7…) Q. How can I make a histogram of cortical thickness? A: In Matlab you can use the read_curv() function, as in the example below. * thick = read_curv ('/usr/local/freesurfer/subjects/bert/surfer/lh.thickness'); hist (thick,100); Notice that there are many zero values that refer to areas where there's no cortical surface. The best procedure is to create a new array without the zero values and then make the histogram. The matlab code are just in these three lines. thick = read_curv(bert); fileID2 = fopen(outfile,'w'); fprintf(fileID2,'%s \n',thick); The first image below shows the first 500 thicknesses in the array while the second image shows the first 5,000. There is a distinct oscillation/periodicity in the data that is written out. We were wondering if this has to do with the way that FS rasters across the brain going from sulci to gyri, etc? If the data is placed in a histogram, in a normal control subject we do get and expect a Gaussian distribution. Please let us know! Thanks, Jon [cid:image001.png@01DC39D4.C0D9EE30] [cid:image002.png@01DC39D4.C0D9EE30] Jonathan P. Dyke, Ph.D., DABMP (MRI) Professor of Physics Research in Radiology Weill Cornell Medicine Citigroup Biomedical Imaging Center 516 East 72nd Street, New York, NY 10021 T: (212) 746-5781 jpd2001(a)med.cornell.edu<mailto:jpd2001@med.cornell.edu> https://secure-web.cisco.com/10j0E5YHOxocBnWfcrDQ216C6nsc2hKJWtNPtq-wJom6Ys…<https://secure-web.cisco.com/1Lnkj1qw7ihDOCfmxSKCVFoSzRb4AchVJ4tZveXJcU8yLE…> https://secure-web.cisco.com/1Vk4ZlA8td_XcHqE_xIWYF3DPPZztt5RTvnCLZOXo3Xbv-… https://secure-web.cisco.com/11foGvXt-9ehohguhfB8iiX-faywHX81Sf7kmgUKGn3FBA…

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