Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30070 discussions

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…; . 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. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu 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 https://secure-web.cisco.com/1fxc1lsFwviJlioOzsd96KzOOWLpfCxubigEzaM9nvWS8T… <https://secure-web.cisco.com/1Z5pHueRBOlx1_n8rqBTNJNUCHbxhy0PUyW4Zmn7WSvXAEijRczwJqomMxAOtMt3ZWBN2SHmIZDIUHtqrUoc9OpvSmJnhclVHFGP8WWFrq2y_Vd4bBB5hc84Zl90WC8fWcSICs8ltsAS5_QqSAGD2njZ0mJ1VUG2l6EBDrHxaE9yq4UWCa4ImvjjqaMd0zQ1GQ9ohVSskhssGwkWWcIM6YeHNtEZW7mgD26QJ6H_fjI6za-KyHgd4s0xpTNCw3SBPz3haqI2oWZux8eF90jtsR2YD38MIRfAtBWhovI-LtXM_yZTQApf_qQP45FVftX9gYH_NcK2263VQiacT1cM8Qg/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . 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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Out of Office
by June Kang 22 Feb '25

22 Feb '25

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Question regarding high Disk IO during Local Gyrification Index calculations,
by Ha, Sung Min 22 Feb '25

22 Feb '25

External Email - Use Caution Hello, I am running (recon-all -localGI) command on around ~250 subjects concurrently right now on high performance computing cluster running SLURM using FreeSurfer 6.0. These subjects already have recon-all finished and I am running recon-all -localGI to additionally calculate LGI values per subject. The cluster manager got back to me stating that these jobs are causing massive amount of IOPs on the storage to the point of slowing down the entire cluster to unusable state. Is this expected behavior with LGI calculation? Is there any flag I can pass to recon-all to reduce the intermediate files being written and read during the calculations? Any help or advice would be greatly appreciated. Sincerely, Sung

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Hippocampus and amygdala segmentation
by Miguel Ángel Rivas Fernández 21 Feb '25

21 Feb '25

External Email - Use Caution Dear Eugenio, My name is Miguel. I am currently processing data of the ABCD Study using FreeSurfer. In our pipeline, we also include the specific FreeSurfer segmentations for the hippocampus and amygdala. As an additional step, we would like to use these segmentations as masks. However, I see that FreeSurfer exports several files, and I am not entirely sure which one I should use. From what I read on the wiki, the files with the suffix *FSvoxelSpace.mgz* are the segmentations that are in the same voxel space as the other FreeSurfer volumes, although it is noted that these segmentations are somewhat rougher. However, I see that there are several files with that name. For example, for the hippocampus segmentation in both hemispheres, we have: - *CA.FSvoxelSpace* - *FS60.FSvoxelSpace* - *FSvoxelSpace.mgz* - *HBT.FSvoxelSpace.mgz* I would like to have an image that contains all hippocampus and amygdala segmentations in a single image. In that case, which file should I use? Perhaps *FSvoxelSpace.mgz*? Another question arises, not only for the hippocampus segmentation but also for other segmentations. Is there a list on the FreeSurfer wiki that shows which region corresponds to each value in the segmentations? For example, in the file *lh.hippoAmygLabels-T1.v22.FSvoxelSpace.mgz*, the value 2000 corresponds to structure X. I am also interested in this labeling for the thalamus and brainstem segmentations (for the hypothalamus, I see that they are listed in a table on the website: [ https://secure-web.cisco.com/1Ri4u8JcCgMmT8lkhPiOD8Jt189NZVInJMJiY327a8k4d2… ). Thank you very much! Miguel

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Re: [Freesurfer] *** buffer overflow detected ***
by fsbuild 21 Feb '25

21 Feb '25

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 https://secure-web.cisco.com/1YUhZcLLpg4GoPqDFoZq91udJaMJb659sWfNv6Mp1j4MmR…

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Re: [Freesurfer] Unable to download version 8.0.0
by fsbuild 20 Feb '25

20 Feb '25

External Email - Use Caution  The web pages are being updated in advance of the release, but the download links won’t go live until sometime after 8.0.0 has been officially announced on the mailing list. - R. On Feb 20, 2025, at 07:11, Ziming Cui-MSBA23A <zimingc3(a)uci.edu> wrote:        External Email - Use Caution        Hello all,  I'm trying to download version 8..0.0 of the “macOS X darwin_arm64 (64b) PKG installer”, but it says “Not Found” no matter what I try. Is there anything I can do? Best,By Ziming Cui_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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