Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

Visualizing brain features
by Banerjee, Tania 16 Sep '24

16 Sep '24

External Email - Use Caution Hello, I have a quick question regarding my pial analysis, which, after feature selection, includes regions such as lh_G_temp_sup-G_T_transv_area and lh_S_interm_prim-Jensen_area, among others. Is there a method or tool available to visualize these specific brain areas? If not, I would appreciate any guidance to locate these areas in a standard brain structure. Thank you, Tania Banerjee

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mri_synthseg on Mac M3
by Valerian Altersberger 15 Sep '24

15 Sep '24

External Email - Use Caution Dear Freesurfer Community, I am new to using Freesurfer and obtained version 7.4.1 to try white and grey matter segmentation with the help of mri_synthseg. I am running it on an Apple M3 chip under Sonoma 14.5. However, if I try to run mri_synthseg I get the error “illegal instruction”. I also tried to run Freesurfer 7.4.1 in Docker using the x86 (amd64) architecture but when trying the command mri_synthseg I still receive the error “illegal instruction”. Also, opening the terminal using Rosetta did not change the outcome. I would very much appreciate your help and avice. Kind regards, Valerian Altersberger

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Re: [Freesurfer] Ongoing issue with Mac
by fsbuild 13 Sep '24

13 Sep '24

External Email - Use Caution I mistkamely put the .tgz archive for the Intel Mac instead of its ,pkg file in the red box in the screenshot. - R. On Sep 13, 2024, at 22:35, fsbuild <fsbuild(a)contbay.com> wrote:        External Email - Use Caution         When you navigate in a browser to,https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/- you choose to download the installer package for either an Intel processor Mac (freesurfer-macOS-darwin_x86_64-dev.pkg) or a Silicon Mac with an M1, M2, M3 chip (freesurfer-macOS-darwin_arm64-dev.pkg). My browser preferences are set to ask whether or not to download a file when clicking on a link (see screenshot).  You may not see that if your browser is set to block pop-up windows, or you might have some other setting blocking downloads, but I can download either package file.  Those files can be refreshed periodically, so you may have to reload the web page in your browser if you have not looked at it recently. But the link should always work. After you have downloaded the .pkg installer and clicked on it to install as described in the previous maill, you should check freeview can open an empty window from the terminal, i.e., don’t try to display and volumes or surfaces. You should see something like what’s listed below when setting up the freesurfer environment in the terminal window. $ bash$ export FREESURFER_HOME=/Applications/freesurfer/dev$ source $FREESURFER_HOME/SetUpFreeSurfer.sh———— freesurfer-macOS-darwin_x86_64-dev-20240909-9ca95c6 ————    <—— this is from the install of the Intel Mac .pkgSetting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME.       /Applications/freesurfer/devFSFAST_HOME                /Applications/freesurfer/dev/fsfastFSF_OUTPUT_FORMAT    nii.gzSUBJECTS_DIR                 /Applications/freesurfer/dev/subjectsMNI_DIR                          /Applications/freesurfer/dev/mni $ which freeview/Applications/freesurfer/dev/bin/freeview$ freeview                                                       <—— this should open an empty freeview window If you get the empty window, then freeview is basically working. - R. On Sep 13, 2024, at 20:24, Alisha Davis <davis.alisha1999(a)gmail.com> wrote:       External Email - Use Caution         Hello, I sent an email regarding issues with not being able to get the newest version (or any version, really) of freesurfer to run on my Mac due to the fact that no update can handle MacOS version 14.5. I just received another email from Henry that was sent to an individual having a similar issue, and the link for the download does not work for me yet again. I keep receiving messages that the server cannot be found. I can get the download onto my Mac, but every time I open an MRI, the program immediately crashes. Im not sure if there is another link to try or one with a server that can be found, but any help would be appreciated! Cheers, Alisha _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard..edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <mac_pkg_download.png>_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Ongoing issue with Mac
by fsbuild 13 Sep '24

13 Sep '24

External Email - Use Caution  When you navigate in a browser to,https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/- you choose to download the installer package for either an Intel processor Mac (freesurfer-macOS-darwin_x86_64-dev.pkg) or a Silicon Mac with an M1, M2, M3 chip (freesurfer-macOS-darwin_arm64-dev.pkg). My browser preferences are set to ask whether or not to download a file when clicking on a link (see screenshot).  You may not see that if your browser is set to block pop-up windows, or you might have some other setting blocking downloads, but I can download either package file.  Those files can be refreshed periodically, so you may have to reload the web page in your browser if you have not looked at it recently. But the link should always work. After you have downloaded the .pkg installer and clicked on it to install as described in the previous maill, you should check freeview can open an empty window from the terminal, i.e., don’t try to display and volumes or surfaces. You should see something like what’s listed below when setting up the freesurfer environment in the terminal window. $ bash$ export FREESURFER_HOME=/Applications/freesurfer/dev$ source $FREESURFER_HOME/SetUpFreeSurfer.sh———— freesurfer-macOS-darwin_x86_64-dev-20240909-9ca95c6 ————    <—— this is from the install of the Intel Mac .pkgSetting up environment for FreeSurfer/FS-FAST (and FSL)FREESURFER_HOME.       /Applications/freesurfer/devFSFAST_HOME                /Applications/freesurfer/dev/fsfastFSF_OUTPUT_FORMAT    nii.gzSUBJECTS_DIR                 /Applications/freesurfer/dev/subjectsMNI_DIR                          /Applications/freesurfer/dev/mni $ which freeview/Applications/freesurfer/dev/bin/freeview$ freeview                                                       <—— this should open an empty freeview window If you get the empty window, then freeview is basically working. - R. On Sep 13, 2024, at 20:24, Alisha Davis <davis.alisha1999(a)gmail.com> wrote:       External Email - Use Caution         Hello, I sent an email regarding issues with not being able to get the newest version (or any version, really) of freesurfer to run on my Mac due to the fact that no update can handle MacOS version 14.5. I just received another email from Henry that was sent to an individual having a similar issue, and the link for the download does not work for me yet again. I keep receiving messages that the server cannot be found. I can get the download onto my Mac, but every time I open an MRI, the program immediately crashes. Im not sure if there is another link to try or one with a server that can be found, but any help would be appreciated! Cheers, Alisha _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Ongoing issue with Mac
by Alisha Davis 13 Sep '24

13 Sep '24

External Email - Use Caution Hello, I sent an email regarding issues with not being able to get the newest version (or any version, really) of freesurfer to run on my Mac due to the fact that no update can handle MacOS version 14.5. I just received another email from Henry that was sent to an individual having a similar issue, and the link for the download does not work for me yet again. I keep receiving messages that the server cannot be found. I can get the download onto my Mac, but every time I open an MRI, the program immediately crashes. Im not sure if there is another link to try or one with a server that can be found, but any help would be appreciated! Cheers, Alisha

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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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