Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

Freesurfer 7.4.0 and CUDA versions (was Re: (no subject))
by fsbuild 12 Sep '24

12 Sep '24

External Email - Use Caution  The 7.4.0 release contains the python distribution all the python scripts (including mri_synthseg) were tested with (on CentOS 8, 7; Ubuntu 22, 20 18).  That python includes tensorflow 2.12.0 which is documented to support up thru Cuda 11.8.   If you look at all the cuda libraries you will see their major release numbers range from 8-11.  Since older libraries may be backwards compatible, I suggest you try installing Cuda 11 on your system and see if it is recognized. - R. On Sep 9, 2024, at 22:31, Matthew Lynch <matthewl077(a)gmail.com> wrote:        External Email - Use Caution         I run this command:  mri_synthseg --i /mnt/p/test/test-t2-3mm.nii --parc --robust --o /mnt/p/test and it fails with the following (partial) error message: Node: 'model_3/unet_conv_downarm_0_0/Conv3D' DNN library is not found. which I assume means it cannot access the appropriate the CuDNN library. I have installed GPU: nvidia geforce RTX 3050 Ti (4Gb) WSL2 Linux kernel: 5.15.153.1-microsoft-standard-WSL2 (after recent wsl --update) CUDA Version 12.6 Windows Nvidia Driver version 560.94 CuDNN Version 9.4.0 installed in WSL, with libraries located in /lib/x86_64-linux-gnu However, freesurfer's tensorflow seems to point to its own cudnn libraries in: /usr/local/freesurfer/7.4.0/python/lib/python3.8/site-packages/nvidia/cudnn/lib including libcudnn.so.8  which I assume is CuDNN version 8, and may not be compatible with CUDA 12.6? Is there a way I can get freesurfer's script to use the CuDNN 9.4.0 that are installed globally on the WSL system?  Any other suggestions on what might be causing this error and how to fix it? _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] SAMSEG - hanging for FLAIR lesion segmentation
by Sravanthi Upadrasta 11 Sep '24

11 Sep '24

External Email - Use Caution Hi Stefan, Thanks for the response. PFA the log. Here is one frame of registration. [image: image.png] Thanks and regards, Sravanthi. On Fri, Sep 6, 2024 at 12:47 PM Stefano Cerri <stce(a)di.ku.dk> wrote: > Hi Sravanthi, > > > Can you check that "template_coreg.mgz" produced by samseg is aligned > with your FLAIR image? There might be an issue with the initial template > registration. If that is not the case, can you provide the full SAMSEG log? > A warning might have been issued before it hung there. > > > Stefano > > > [Freesurfer] SAMSEG - hanging for FLAIR lesion segmentation > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj…> > > Sravanthi Upadrasta > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> > Thu, 05 Sep 2024 04:46:51 -0700 > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> > > External Email - Use Caution > > Hi, > > I am encountering an issue with Samseg while extracting lesion information > from a CUBE FLAIR image. The process hangs for a long time and I have to > forcekill the process after almost 2 hours. I did not have this issue with > same subject T1w and T2 FLAIR images. > Freesurfer - 7.2.0 > Ubuntu 20.04 > > Read mesh collection: > /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz > Transforming points > Transforming points > Read mesh collection: > /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz > Read mesh collection: > /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz > > Could you help me troubleshoot this? > > Thanks, > Sravanthi. > > _______________________________________________ > Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > 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://www.massgeneralbrigham.org/complianceline > <https://www.massgeneralbrigham.org/complianceline> . > 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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Re: [Freesurfer] Installer for Silicon M1, M2, M3 Macs (was Re: Freesurfer for MacOS))
by fsbuild 10 Sep '24

10 Sep '24

External Email - Use Caution Single (left) click on the link to download.  Then after the file is on your machine, e.g., in the Downloads folder, right click and hold and select the option for installer.app (default).  On Sep 10, 2024, at 12:21, Alisha Davis <davis.alisha1999(a)gmail.com> wrote:        External Email - Use Caution        When I right-click on that link, I do not get the option to download with the installer.app. Are there any other prerequisite steps to this? Cheers,Alisha On Sep 9, 2024, at 4:56 PM, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution         If you are using a Silicon Mac with an M1, M2, M3 chip, then please download and install the arm64 freesurfer development .pkg installer via the link,  freesurfer-macOS-darwin_arm64-dev.pkg Right click on the file freesurfer-macOS-darwin_arm64-dev.pkg and select “Open with —> installer.app (default)” which should bypass some of the security warnings.  Then follow the prompts to install (you will need to enter an admin password). Then setup the freesurfer environment as usual, setting FREESURFER_HOME, sourcing the setup script.  Using this installer should avoid any error messages with “illegal instruction" from running the Intel binaries, e.g., from the 7.4.1 release. - R. On Sep 9, 2024, at 19:19, Alisha Davis <davis.alisha1999(a)gmail.com> wrote:       External Email - Use Caution         Hello, My name is Alisha Davis, and I have been using Freesurfer over the past few weeks for an MRI project but have encountered a few issues due to the version of my computer. Is there a plan to release a newer version of Freesurfer compatible with newer MacOS versions, or should I resort to reverting the update on my computer? I look forward to hearing back from you. Thank you, Alisha Davis _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Installer for Silicon M1, M2, M3 Macs (was Re: Freesurfer for MacOS))
by fsbuild 10 Sep '24

10 Sep '24

External Email - Use Caution  If you are using a Silicon Mac with an M1, M2, M3 chip, then please download and install the arm64 freesurfer development .pkg installer via the link,  freesurfer-macOS-darwin_arm64-dev.pkg Right click on the file freesurfer-macOS-darwin_arm64-dev.pkg and select “Open with —> installer.app (default)” which should bypass some of the security warnings.  Then follow the prompts to install (you will need to enter an admin password). Then setup the freesurfer environment as usual, setting FREESURFER_HOME, sourcing the setup script.  Using this installer should avoid any error messages with “illegal instruction" from running the Intel binaries, e.g., from the 7.4.1 release. - R. On Sep 9, 2024, at 19:19, Alisha Davis <davis.alisha1999(a)gmail.com> wrote:       External Email - Use Caution         Hello, My name is Alisha Davis, and I have been using Freesurfer over the past few weeks for an MRI project but have encountered a few issues due to the version of my computer. Is there a plan to release a newer version of Freesurfer compatible with newer MacOS versions, or should I resort to reverting the update on my computer? I look forward to hearing back from you. Thank you, Alisha Davis _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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NIH R25 Course : Training in Advanced Statistical Methods in Neuroimaging and Genetics, Salt Lake City, Utah, April 7-18, 2025.
by ROBERT CARY WELSH 10 Sep '24

10 Sep '24

External Email - Use Caution Hi everybody, We are pleased to announce that the application portal is open for the NIH funded 2025 session of the course, “Training in Advanced Statistical Methods in Neuroimaging and Genetics”. We hope you pass this email on to your local neuroimaging community. The course will start on Monday, April 7th, 2025 and finish on April 18th, 2025 and is to be held in person, in Salt Lake City, Utah, United States at the University Guest House Conference Center. Our course also includes an ongoing (throughout the year) continuing education portion. The course is an intensive 2-weeks, about 8 hours per day of a balanced mixture of lectures and hands-on computer labs. neurostatsbootcamp.org<http://neurostatsbootcamp.org/> Due to recently increased funding, we are pleased to announce we can continue to offer the course for $2250 (from $3000). Strictly financial need scholarships are also offered (that offset even more tuition). Tuition includes hotel accommodations at the University Guest House (arrival on April 6 with departure on April 18), breakfast, lunch, day time snacks, three dinners out as a group, and the planned evening activities. All course attendees will arrange for their own transportation to Salt Lake City. The course cost does include a daily pass to the Salt Lake City Trax light rail/commuter system. (Please note that the course instructors' effort is supported by the NIH grant thus avoiding that cost being passed on to the course attendees. This course is strictly not-for-profit.) Because of the limited size and advanced nature of the course, attendance is by application only – please make sure to fully read the website instructions. In general, applicants should be a US citizen, permanent resident, or working with an appointment at a US institution, though we do have the ability to accommodate 3 to 6 individuals that do not meet this criteria. We anticipate the total class size to be between 24 and 30 students. There are opportunities for scholarships which can partially offset hotel accommodations. These are based on true financial need and you will be instructed how to apply if you are admitted to the course. We look forward to seeing you in SLC in 2025! Priority application deadline is Oct 25, 2024; decisions around Dec 13th. Late application deadline is Nov 22, 2024; decisions by Jan 3th, 2025. For more information email us at neurostats(a)g.ucla.edu<mailto:neurostats@g.ucla.edu> Robert and Anna ------------------------------ Robert Welsh, PhD Course Director, Training in Advanced Statistical Methods in Neuroimaging and Genetics rcwelsh(a)g.ucla.edu<mailto:rcwelsh@g.ucla.edu> (preferred) robert.c.welsh(a)utah.edu<mailto:robert.c.welsh@utah.edu> Anna Docherty, PhD Associate Course Director, Training in Advanced Statistical Methods in Neuroimaging and Genetics anna.docherty(a)utah.edu<mailto:anna.docherty@utah.edu> Christina Caldera Course Administrator neurostats(a)g.ucla.edu<mailto:neurostats@g.ucla.edu>

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Freesurfer for MacOS
by Alisha Davis 09 Sep '24

09 Sep '24

External Email - Use Caution Hello, My name is Alisha Davis, and I have been using Freesurfer over the past few weeks for an MRI project but have encountered a few issues due to the version of my computer. Is there a plan to release a newer version of Freesurfer compatible with newer MacOS versions, or should I resort to reverting the update on my computer? I look forward to hearing back from you. Thank you, Alisha Davis

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Re: [Freesurfer] installation on Linux server incompatible with python2?
by fsbuild 09 Sep '24

09 Sep '24

External Email - Use Caution  You could try first installing rocky8, then install freesurfer, then *upgrade* the machine to rocky9, though you still may not have python2 after the upgrade.   We have not run into any issues so far running the freesurfer rocky8 binaries on rocky9. You could try using the —skip-broken switch when you install the RPM directly on rocky9. You could try downloading/building python2 directly on the Rocky9 machine, i.e., see this thread with same issue on CentOS9,https://stackoverflow.com/questions/71256853/how-do-i-install-pytho… - R. On Sep 9, 2024, at 17:48, Gowin, Joshua <JOSHUA.GOWIN(a)cuanschutz.edu> wrote:        External Email - Use Caution        Hello FreeSurfer community,    We are trying to install FreeSurfer on a new server that uses Rocky Linux 9.4 (Blue Onyx). Unfortunately, python2 is not available on this Linux version, but we believe it is necessary to run FreeSurfer.Are there possible FreeSurfer builds that do not require python2? Or would it be better to run FreeSurfer from a container image based on Rocky 8, which still has Python2 available?Or, are there other solutions that would be better for us?  We’d be grateful for any suggestions for our set up.  Josh  _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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installation on Linux server incompatible with python2?
by Gowin, Joshua 09 Sep '24

09 Sep '24

External Email - Use Caution Hello FreeSurfer community, We are trying to install FreeSurfer on a new server that uses Rocky Linux 9.4 (Blue Onyx). Unfortunately, python2 is not available on this Linux version, but we believe it is necessary to run FreeSurfer. Are there possible FreeSurfer builds that do not require python2? Or would it be better to run FreeSurfer from a container image based on Rocky 8, which still has Python2 available? Or, are there other solutions that would be better for us? We'd be grateful for any suggestions for our set up. Josh

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UNABLE TO MAKE EDITS AFTER SIMNIBS
by Cesar Zabdiel Gutierrez Mendoza (czgtrrzm) 09 Sep '24

09 Sep '24

External Email - Use Caution Hello to all, I am attempting to do a simple editing on Freesurfer where I just want to do manual voxel editing. I am working off of the “Ernie” model from SimNibs. I ran charm on simnibs to get a mesh. After I received the mesh, I used the “labeling_tissues_upsampled.nii.gz” and attempted to edit. When I attempt to edit, there simply is not a response on the screen itself. I left click and drag but it does not let me edit. P.S. I have been able to edit other models when I do not run it through SIMNIBS. Anyone got tips about running things through SIMINBS? Could it be permission error? Could it be something else? Let me know. Using an M1 Macbook Air. On newest software Please let me know if you have suggestions!

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How do we account for different scanner/acquisition parameters in the FreeSurfer longitudinal pipeline?
by Yoonho Hwang 08 Sep '24

08 Sep '24

External Email - Use Caution Dear FreeSurfer team, We are using the Freesurfer longitudinal pipeline, and we had questions about accounting for different scanners and acquisition parameters. We are looking at 3 different timepoints with 2 different scanners (scanner 1 was used for time points 1 and 2, scanner 2 was used for time point 3). Timepoint 1 (scanner1, 512 x 512 x 244 or 512 x 512 x 180) Timepoint 2 (scanner1, 512 x 512 x 180) Timepoint 3 (scanner2, 448 x 448 x 192 or 448 x 448 x 208) Q1: Does creating the subject template based on median and intensity scaling help address the issue of different scanners and acquisition parameters when conducting longitudinal analyses? If it is not sufficient to address the scanner/acquisition issue, do you have any recommendations as to next steps to account for this? We have seen others use LongCombat harmonization or linear mixed effects models to address this issue, is that something you would consider as well? Q2: In a similar vein, when we received the warning below in the "base" step of longitudinal analysis, we were wondering how much it was affecting our results. Would it be helpful to resample the images? Do you have suggestions on other avenues we could consider to address this warning and have robust and reliable results? ************************************************************ ******************* WARNING: Image parameters differ across time, maybe due to aquisition changes? Consistent changes in, e.g., resolution can potentially bias a longitudinal study! You can check image parameters by running mri_info on each input image. Will continue in 10 seconds ... ************************************************************ ******************* Thank you Sincerely, Yoonho -- *Hwang, Yoonho* *Research professor* *Institute of Human Genomic Study,* *College of Medicine, Korea University* *#123, Jeokgeum-ro, Danwon-gu, Ansan-si, Gyeonggi-do, **15355, Republic of Korea.* *Email: ken.lmstar11(a)gmail.com <ken.lmstar11(a)gmail.com>*

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