Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

Convert 1D mgh back to 3D
by Melissa Thalhammer 26 Feb '25

26 Feb '25

External Email - Use Caution Dear everyone, I know that this might be not exactly the right place to ask, but I unfortunately did not reach the authors of the publication so far. I want to work with the evolutionary expansion map by Wei et al. published in Nat Comm (2019; https://secure-web.cisco.com/1EOa2cp_XKYtekyLUN3mqm-iZxVh0pAiE-j1_IvELbdew0…) On their website, they provide a download link leading to two mgh files (attached; https://secure-web.cisco.com/1wjBHK0nX5LW0U-Wy1w4rY2bystAnHOCIGlVB_T3xRlPwI…) I read them with the Matlab load_mgh.m function provided here (https://secure-web.cisco.com/1-0OpH0qgfeFpbCMfaVWHm-btTsT6A2ZX44WYfXtCEzjf9…) and it shows a 163842 x 1 vector (which probably corresponds to fsaverage6 I guess...). I now want to convertthe 1D vector back into 3D. I have come across save_mgh.m but don't know what should be put in as M (4x4 vox2ras transform). Any ideas what is the correct way to do that? Thank you! Best, Melissa

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Recon-all: skip initial inhomogeneity correction
by Miguel Ángel Rivas Fernández 25 Feb '25

25 Feb '25

External Email - Use Caution Dear FreeSurfer developers, I am currently working with a T1-weighted MRI dataset that has already undergone intensity inhomogeneity correction. Since I would like to run recon-all on this data, is it possible to include a flag in recon-all to skip this step? If so, could you please specify the correct flag to use in order to run recon-all properly? Thank you very much for your assistance. Best -- *Miguel Ángel Rivas Fernández*

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dt_recon and corregistration (2)...
by Gonzalo Rojas Costa 24 Feb '25

24 Feb '25

External Email - Use Caution Hi: The error is in a misalignment between the FA and CC_Anterior section. Sincerely, Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University

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Re: [Freesurfer] Inquiry Regarding FreeSurfer Usage in Clinical Trials
by fsbuild 24 Feb '25

24 Feb '25

External Email - Use Caution  If you have not looked at the Freesurfer license terms (which you agreed to when you downloaded the software),https://secure-web.cisco.com/1TLtJ8aYiTR8TmbT0XIgGWuiazFxBl5kXBTS… - then you should note the following in Part B, section (e), number 4, 4. The Software has been designed for research purposes only and has   not been reviewed or approved by the Food and Drug Administration   or by any other agency. YOU ACKNOWLEDGE AND AGREE THAT CLINICAL   APPLICATIONS ARE NEITHER RECOMMENDED NOR ADVISED. Any   commercialization of the Software is at the sole risk of the party   or parties engaged in such commercialization. You further agree to   use, reproduce, make derivative works of, display and distribute   the Software in compliance with all applicable governmental laws,   regulations and orders, including without limitation those relating   to export and import control.. I am not aware of any reviews by the FDA (or from other government agencies) that have approved freesurfer for clinical use. Although the MGH license is essentially open source allowing use/re-distribution of the software, it is however subject to the license restrictions of the included 3rd party code as noted in Part B, section (e), number 3, 3. This Software License does not grant any rights with respect to   third party software, except those rights that MGH has been   authorized by a third party to grant to you, and accordingly you   are solely responsible for (i) obtaining any permissions from third   parties that you need to use, reproduce, make derivative works of,   display and distribute the Software, and (ii) informing your   sublicensees, including without limitation your end-users, of their   obligations to secure any such required permissions. Those 3rd party licenses can be found under ,https://secure-web.cisco.com/1q3oL4x5gqV_bdyKyRolyR9hw97oWH5oVRLzSotDPItR5GWo823uPbDV-qbLIcPZi8yiKAsU1U_3qYiRT_Va1aCW8kYvMGtM3jewxPEYAM_OWt6LJ-nf7BYt9279pXEW5w6ytY_kai534Hlz3AmWimuXTGoeTBrXfSLAHmF9u_X_s1HVaqVNZMFp3LrusDh5D07g0HMxg3IzGAXQNfjdpgMxjgAU4f6sXQ_BCAEs-woKvihQrDATyl4a3t594Z5EmrefAzESjgEm9sh1_CJAPyXgNXA73iOlV_qAB4a6m25Xtk_i1XZjaHMZTkmVmBhoYtkHO21npxrKPN1jdUtQtKQ/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Ftree%2Fdev%2Fdistribution%2Fdocs Some of those licenses may stipulate that once their 3rd party code in freesurfer is used in a commercial/for profit setting, then a paid for commercial license would need to be negotiated with the copyright holder. Freesurfer 6 is about ~7 years old now.  Freesurfer 7 releases were made available from 2020 thru 2023 with the last release as 7.4.1 in June of 2023.  Freesurfer 8.0.0 is about to be released (February 2025).   You can see the current releases here,https://secure-web.cisco.com/18FWAuTV9mgC0-k8_UudIcvI2UfmRMWvQDPOWoIWh… It would not surprise me if there was no point now in trying to get Freesurfer 6 approved for clinical trials because it will not run on recent versions of Linux OS’s. - R. On Feb 19, 2025, at 04:58, Yeh Shang Ming <yeh(a)micron-kobe.com> wrote:        External Email - Use Caution        Dear Sir/Madam, My name is Shang-Ming (Tony) Yeh, and I work at an imaging CRO based in Japan. We are currently using FreeSurfer version 6.0.0 and are considering its use in a potential project. To support our evaluation, we would appreciate your insights on the following:Clinical Trial Usage: - Has FreeSurfer been utilized in any clinical trials? - If so, have any of these trials been submitted for regulatory approval? Comparative Studies:- Are there any publications that compare FreeSurfer with other similar software?If you have any relevant information or publications, we would greatly appreciate it if you could share them with us. Thank you for your time and support. We look forward to your response. Sincerely,Shang-Ming (Tony) Yeh_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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dt_recon and corregistration...
by Gonzalo Rojas Costa 24 Feb '25

24 Feb '25

External Email - Use Caution Hi: I used the following commands: dt_recon --i sub-OAS30003_ses-d1631_run-01_dwi.nii.gz --b sub-OAS30003_ses-d1631_run-01_dwi.bval sub-OAS30003_ses-d1631_run-01_dwi.bvec --s OAS30003_MR_d1631 --o dt_recon_result cd dt_recon_result mri_vol2vol --mov lowb.nii.gz --targ $SUBJECTS_DIR/OAS30003_MR_d1631/mri/aseg.mgz --inv --interp nearest --o $SUBJECTS_DIR/OAS30003_MR_d1631/mri/aseg2diff.mgz --reg register.dat --no-save-reg mri_segstats --seg $SUBJECTS_DIR/OAS30003_MR_d1631/mri/aseg2diff.mgz --ctab /home/gonzalorojascosta/freesurfer/FreeSurferColorLUT.txt --i fa.nii.gz --sum fa.stats And, to view the results, I used: freeview -v $SUBJECTS_DIR/OAS30001_MR_d0757/mri/brain.mgz $SUBJECTS_DIR/OAS30001_MR_d0757/mri/orig.mgz $SUBJECTS_DIR/OAS30001_MR_d0757/mri/aseg.mgz:colormap=lut:opacity=0.2 fa.nii.gz:reg=register.dat:colormap=heat -colorscale -viewport coronal Why is there a major error with the FA in CC_Anterior section (see attached image)? Sincerely Gonzalo M. Rojas-Costa Adjunct Assistant Professor School of Medicine Finis Terrae University

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Re: [Freesurfer] Licensing & permission for publication
by fsbuild 24 Feb '25

24 Feb '25

External Email - Use Caution  Someone familiar with legal/licensing issues can check the terms of license found here,https://secure-web.cisco.com/1NpU4HWkbrw7VB72lxFKWX3QRK_rGCpFVO86h8MKv… B section 1 may be of interest, PART B. DOWNLOADING AGREEMENT - License from MGH with Right to Sublicense("Software License"). 1. As used in this Software License, "you" means the individual   downloading and/or using, reproducing, modifying, displaying and/or   distributing the Software and the institution or entity which   employs or is otherwise affiliated with such individual in   connection therewith. The General Hospital Corporation ("MGH")   hereby grants you, with right to sublicense, with   respect to MGH's rights in the software, and data, if any,   which is the subject of this Software License (collectively, the   "Software"), a royalty-free, non-exclusive license to use,   reproduce, make derivative works of, display and distribute the   Software, provided that:   … list of conditions follow … If you agree with/adhere to the license conditions, then my (non-lawyer) interpretation of the above is that you are allowed to display (publish) the output from freesurfer commands/processes and/or display templates/files that you use.   You could also cite something to the effect that Freesurfer is licensed by the MGH corporation of Boston MA, USA with the above link to the license. - R. On Feb 24, 2025, at 16:45, Brown, Tanya <tanya.brown.extern(a)ae.mpg.de> wrote:        External Email - Use Caution        I am writing on behalf of our research team regarding our upcoming publication of our study, in which we would like to include results figures that were output from Freesurfer software (specifically the fsaverage template in Freesurfer). As we prepare our manuscript for publication, we have encountered a licensing issue. Specifically, the journal has indicated that we need to seek permission for figures where we use Freesurfer brain templates.   Have you encountered similar challenges when publishing figures that feature images from your software? If so, could you kindly share the approach or any guidelines you followed to comply with the licensing terms while still effectively presenting our findings? Any advice or suggestions you could provide would be greatly appreciated, as it would help us determine the best path forward and ensure that we adhere to the necessary legal and ethical standards. Please note, we have cited the inaugural paper: Fischl, B. (2012). FreeSurfer. NeuroImage, 62(2), 774–781. Thank you very much for your time and assistance. I look forward to your guidance. Tanya_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail..nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Licensing & permission for publication
by Brown, Tanya 24 Feb '25

24 Feb '25

External Email - Use Caution I am writing on behalf of our research team regarding our upcoming publication of our study, in which we would like to include results figures that were output from Freesurfer software (specifically the fsaverage template in Freesurfer). As we prepare our manuscript for publication, we have encountered a licensing issue. Specifically, the journal has indicated that we need to seek permission for figures where we use Freesurfer brain templates. Have you encountered similar challenges when publishing figures that feature images from your software? If so, could you kindly share the approach or any guidelines you followed to comply with the licensing terms while still effectively presenting our findings? Any advice or suggestions you could provide would be greatly appreciated, as it would help us determine the best path forward and ensure that we adhere to the necessary legal and ethical standards. Please note, we have cited the inaugural paper: Fischl, B. (2012). FreeSurfer. NeuroImage, 62(2), 774–781. Thank you very much for your time and assistance. I look forward to your guidance. Tanya

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Optimizing FreeSurfer for Mouse brain
by Ramesh Babu 24 Feb '25

24 Feb '25

External Email - Use Caution Dear Experts, Could you please suggest to me how to optimize FreeSurfer for 3D MRI Mouse Brain analysis? Regards Ramesh

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histo atlas and sTIV
by Antonio Napolitano 24 Feb '25

24 Feb '25

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Re: [Freesurfer] *** buffer overflow detected ***
by fsbuild 24 Feb '25

24 Feb '25

External Email - Use Caution  If I understand the recon-all script correctly, the default is to run with -openmp 1 and even if you were to instead specify the available -DoParallel option, that would set openmp to 4 threads (and itkthreads to 4) to do work in parallel.   I don't run recon-all with options that increase the number of threads beyond the defaults because it is not cluster friendly.  But even for the default settings, you need ~16G of system RAM to run the Ubuntu 22 OS, freesurfer 7.4.1 running recon-all and whatever other processes run on the machine. Given that you specified -openmpi 8, i.e., you added 7 more threads with ~16G of physical RAM to spare, then even with memory management it could be a memory underrun occurred causing the process to exit with Signal 6, e.g., memory allocation fails.   You could try and profile machine resource usage by keeping a program like "glances" running on the console and see if reports critical errors in memory usage, CPU load, etc., while recon-all runs.  Maybe try the DoParallel option instead to see if the machine has enough resources to run that.. - R. On 2/21/25 06:10, Brunno M. de Campos (brunno(a)unicamp.br) wrote:         External Email - Use Caution         Hi,I would also like to include here the entire set of lines I am using. Since there are three different parallel-associated flags for recon-all, I am also concerned about my choice (OpenMP). >> recon-all -i Sub_1_Time_1.nii -subjid Sub_1_Time_1 -qcache -sd ./OUTPUT_DIR -all -openmp 8>> recon-all -i Sub_1_Time_2.nii -subjid Sub_1_Time_2 -qcache -sd ./OUTPUT_DIR -all -openmp 8 >> recon-all -base ./OUTPUT_DIR/Sub_1_base -tp ./OUTPUT_DIR/Sub_1_Time_1 -tp ./OUTPUT_DIR/Sub_1_Time_2 -sd "./OUTPUT_DIR -all -openmp 8 >> recon-all -long ./OUTPUT_DIR/Sub_1_Time_1 ./OUTPUT_DIR/Sub_1_base -sd ./OUTPUT_DIR -all -openmp 8>> recon-all -long ./OUTPUT_DIR/Sub_1_Time_2 ./OUTPUT_DIR/Sub_1_base -sd ./OUTPUT_DIR -all -openmp 8 Thank you very much! Brunno M Campos University of Campinas Em qui., 20 de fev. de 2025 às 08:50, Brunno M. de Campos <brunno(a)unicamp.br> escreveu: Hi, thanks. > version of freersurfer you are running: 7.4.1> OS name and version you are running: Ubuntu 22> amount of RAM on your machine: 32 gb Best, Brunno M Campos University of Campinas Em qui., 20 de fev. de 2025 às 08:47, fsbuild <fsbuild(a)contbay.com> escreveu:         External Email - Use Caution         Please list: > version of freersurfer you are running> OS name and version you are running> amount of RAM on your machine - R. On Feb 20, 2025, at 05:58, Brunno M. de Campos <brunno(a)unicamp.br> wrote:         External Email - Use Caution         Dear all,I run my script for longitudinal processing based on: individual processing (recon-all -i) + base image creation (recon-all -base) and longitudinal processing (recon-all -long).In some cases (not always), the process terminates with errors, apparently at the same stage. The log states, among other things, "Reading texture...*** buffer overflow detected ***: terminated Command terminated by signal 6".1 - I assume that I have exceeded my memory capacity. Am I correct? I have, in fact, written a script that parallelizes these processes, but I might be distributing the workload poorly if that is the case.2 - If this is indeed the issue, do you know the peak memory required for such a process?Thank you!Brunno M Campos University of Campinas _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/14rLXS-JbgR7AFKonSvLXJI8hjOcdl-HCGj-LG6ZffWz0_… _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/14rLXS-JbgR7AFKonSvLXJI8hjOcdl-HCGj-LG6ZffWz0_… 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 MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1fxc1lsFwviJlioOzsd96KzOOWLpfCxubigEzaM9nvWS8T… <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1Z5pHueRBOlx1_n8rqBTNJNUCHbxhy0PUyW4Zmn7WSvXAE…; . 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