Freesurfer

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30054 discussions

PETSurfer v8.1.0 vs 7.x.x — missing pons in gtmseg.ctab and rescale issue in mri_gtmpvc
by Carme Uribe 22 Oct '25

22 Oct '25

External Email - Use Caution Hi all, I’m running into an issue after upgrading from FreeSurfer 7.1.2 to 8.1.0 when using PETSurfer. In v7.1.2, the gtmseg.ctab included the *pons (Id 174)*, which allowed the subsequent mri_gtmpvc step to perform the default *rescale normalization based on pons intensity*. However, in v8.1.0, the pons no longer appears in the gtmseg.ctab. Since the rescale step still expects that region by default, the pipeline fails when trying to normalize by the pons. From the release notes I see that gtmseg now uses SAMSEG by default, and I suspect that this change may have modified how subcortical or brainstem structures are handled. Also, any chance the gtmseg step could add other regions typically used as reference (e.g., wm/whole cerebellum, centrum semiovale) maintaining the aseg and aparc parcellations from FS? Thanks very much in advance for your help, Carme

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Affine voxel size correction
by Steenwijk, M.D. (Martijn) 22 Oct '25

22 Oct '25

External Email - Use Caution Dear all, Reuter et al. (NI 2010) mention an optional "Affine voxel size correction" as a method to account for slight changes in scanner voxel sizes or geometry. Since it is described as optional, could anyone confirm whether this correction is actually implemented in the longitudinal processing stream? Thank you for your insights. Best regards, Martijn ______________________________________________________ AmsterdamUMC disclaimer : http://secure-web.cisco.com/1P67Snz8AB98mPTZkrythZH-ustg19TKhOwK7sjcvHBR4YG…

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Re: [External] Re: recon-all fails with "Invalid FreeSurfer license key" when executed via Docker SDK but works interactively
by fsbuild 22 Oct '25

22 Oct '25

External Email - Use Caution  I use the interactive option, e.g.,  $ docker run -dit —name <container name> <image name> Everything in the environment works, including using FS_LICENSE with newer versions of freesurfer to find the license file. - R.

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Re: Validation of the thalamic nuclei segmentation
by Kepa Paz-Alonso 21 Oct '25

21 Oct '25

External Email - Use Caution Dear Melissa, I fully agree with Eugenio's view and recommendation. Basically, there has been different historical traditions in regard to thalamic segmentations. You can find attached Figure 19.2 from Mai & Forutan (2012) which shows differences just between some authors in their thalamic nuclei delineation. In other words, different authors have had different conceptions regarding the classification and delineations of thalamic nuclei. For instance, differences are quite notable in some ventral and lateral nuclei, with different territories depending on the classification. And that can apply to other nuclei depending on the classifications you compare. When we started working on our thalamic nuclei atlas (Iglesias et al., 2018), we decided to based our clasification/segmentation on the work done by Jones (2012), which presents quite extraordinary detail in its characterization of the thalamic nuclei. We combined high resolution ex vivo MRI and histology, so the neuroanatomist (Ricardo Insausti) was able to delineate with the best possible precision the different nuclei while having next to him Jones's book to check any detail. So, our atlas and companion segmentation derives from Jones's previous work and it is related to his view regarding thalamic nuclei organization (see Jones, 1998). So, it does not have the same nuclei and the same delineation than other classifications, such as the ones from Morel. In my view, the mentioned "validation" studies from the same first author are comparing things that are conceptually different and are subjected to circularity. As Eugenio pointed out, if you compare different thalamic segmentations to the Morel atlas and our atlas of the thalamus is based on Jones (not Morel) and other ones are based on Morel, which ones are going to look more similar to Morel? But in any case, again these are different conceptual classifications, so if any comparison is done, they need to be done with all the caution. So, as Eugenio mentioned, at this point you can see the advantages or disadvantages or using one or other thalamic nuclei segmentation and go with any of them. There is a consensus among researchers in the neuroscience field regarding the need of bringing a common delineation/classification unifying different coneptual approaches and nomenclatures in thalamic nuclei segmentation. There are plans for having at some point a gathering to work on that. But as far as I know, these are just plans. Hope this can be of any help. Best, Kp. References: Jones, E.G., 2012. The Thalamus. Springer Science & Business Media. Jones, E.G., 1998. Viewpoint: The core and matrix of thalamic organization. Neuroscience. 85 (2): 331– 345 Mai, J.K., Forutan, F., 2012. Thalamus. In: The Human Nervous System, Third Edition. Elsevier, pp. 618–677. - Pedro "Kepa" Paz-Alonso, Ph.D. Group leader, BCBL Ikerbasque Research Professor Ikerbasque Researcher profile Ikerbasque: https://secure-web.cisco.com/176cf5yMCrjsKE7mehNbZbSpwntD7QRGfnXp99NCFtOeY1… Legal disclaimer/Aviso legal/Lege-oharra: http://secure-web.cisco.com/1NwnCoddg-iluZ9xy1tfc8-XzzZjLlqfX7WHql6bxfM4qL4… From: "Iglesias Gonzalez, Juan E.,PHD" <JIGLESIASGONZALEZ(a)mgh.harvard.edu> To: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> Cc: "Pedro Paz-Alonso" <p.pazalonso(a)bcbl.eu> Sent: Friday, October 17, 2025 8:16:59 PM Subject: RE: Validation of the thalamic nuclei segmentation Dear Melissa, I am CCing the senior author Dr. Paz-Alonso so he can also chime in (I wish I could also CC the neuroanatomist that made the annotations, but, sadly, he passed away last year). THOMAS is great but the underlying atlases used Morel as basis for manual segmentation so it is expected that they agree better with the atlas… and, even then, if you look at the Dice scores in the paper, there are plenty of nuclei where FS is higher. I actually find the experiments on AD staging / classification more compelling. Our atlas has the advanrage of working with any MRI contrast “out of the box”, and is pretty good at snapping to the boundaries of the mediodorsal and posterior nuclei (pulvinar), especially if you provide images with good contrast. But if you have images that match the contrast of THOMAS well, then by all means exploit that agreement and use THOMAS! Just my 2 cents 😉 Kind regards, /Eugenio From: Melissa Thalhammer <melissa.thalhammer(a)tum.de> Sent: Friday, October 17, 2025 3:12 AM To: Freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Validation of the thalamic nuclei segmentation External Email - Use Caution Dear FreeSurfers, I read that criticism about the thalamic nuclei segmentation based on T1-images was raised ( DOI: [ https://secure-web.cisco.com/1eJxYpKwA2ZQnNHzMzqolRLQbHC3La8ApnjzLguJLU7IC-… | 10.1016/j.neuroimage.2022.119340 ] and DOI: [ https://secure-web.cisco.com/1Xt62fHdzFAPsCkjEP3euJAJBHslctTFBLGq6CU_IfHiqF… | 10.1162/imag_a_00166 ] ) 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 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/1dXWEfSg2JAqZudeh4s29ZFFfxtrL9p2unTNXkyhgrhM-R… | https://secure-web.cisco.com/13GOIUGGoHrBDNQidkNvxH-Etw6-__vlKLap32IvKeS53M… ] . 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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Applying synthmorph deformations using other tools
by Keith Jamison 20 Oct '25

20 Oct '25

External Email - Use Caution I am trying to apply the synthmorph deformation fields using other tools so that I can combine multiple warps, use spline interpolation, etc. I have tried a few variations of the mri_convert and mri_warp_convert commands, but they either crash or result it skewed or otherwise incorrect outputs. Is there an example out there showing exactly what syntax I should use to convert a synthmorph deform.nii.gz output to something that can work with freesurfer mri_warp_convert, or with FSL or ANTs? -Keith

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SuperSynth installation
by Villagran Asiares, Alberto Gaston 20 Oct '25

20 Oct '25

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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)?

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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…

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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…>

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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

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