Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Password
by Fabien Rech 14 Dec '22

14 Dec '22

External Email - Use Caution Hello I have downloaded the virtual machine FS_7_2_0_Ubuntu_18_04_06.ova.7z <https://secure-web.cisco.com/1qUPe-P47gvxAYMnwB4S_TKKGgEmZnkOOEb9TAZuYqD17f…> from your website. Could you please give me the password to open the archive ? Thank you by advance Best regards Fabien -- Cet e-mail a été vérifié par le logiciel antivirus d'Avast. http://secure-web.cisco.com/1uhdYvZXoI5XlpdwdUTXhO-iPuLM8A4VdaonwEvO6lEEJJo…

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Re: [Freesurfer] High Resolution Freesurfer Error
by Glasser, Matt 13 Dec '22

13 Dec '22

External Email - Use Caution How about a picture of the problem? At least at one time, some of FreeSurfer was limited to 256^3 voxels and there is a maximum resolution that you can fit a human brain in with that. Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Brooklyn Wright <brooklyn.rose14(a)outlook.com> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, December 13, 2022 at 9:18 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] High Resolution Freesurfer Error External Email - Use Caution Hi there 🙂 I am running into repeat difficulty with reconstructing ultra-high resolution T1w .nii images (0.25mm^3 voxel size). These have been submitted to rigorous preprocessing steps and I use hires flags and expert preferences however all of my attempts' output has some part of the brain missing as if it got two-thirds of the way through and then gave up. Have you got any suggestions on how to tackle this? Kindest, Brooklyn. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Archive Passcode Request
by Em Rose Triolo 13 Dec '22

13 Dec '22

External Email - Use Caution Hello, I am installing FreeSurfer on a Windows machine using VirtualBox. I need a passcode to unzip the .ova file. I am emailing to request this passcode. I already have a license txt file, but I am assuming this is something different. Thank you, Em -- Em Triolo (They/Them) Department of Mechanical Engineering: Ph.D. Candidate *University of Washington* M.Eng. Mechanical Engineering- Medical Device Engineering *Stevens Institute of Technology* B.S. Biomedical Engineering *The College of New Jersey*

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lh.pial lh.pialT1n same file?
by Renew Andrade 13 Dec '22

13 Dec '22

External Email - Use Caution Dear experts: I am wondering if lh.pial and lh.pialT1 are the same files. I don’t have lh.pial is that an error from recon-all? Should I rerun recon-all. Or just autorecon-pial? Would that change anything? Best, Rene Andrade.

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Re: [Freesurfer] MacOS Ventura: 7.3.2 release update for only Apple silicon machines (M1/M2 processors)
by fsbuild 12 Dec '22

12 Dec '22

External Email - Use Caution Thanks for the notification the update worked for you on Ventura ;-)  Now that the Ventura 13.0.1 point release is available, we will look at testing on that and/or subsequent releases. - R. On Dec 12, 2022, at 19:59, Sorby-Adams, Annabel <ASORBY-ADAMS(a)mgh.harvard.edu> wrote:Thank you for posting the workaround! Please note this is also working for mri_synthseg on MacOS Ventura (13.0.1). Annabel Annabel Sorby-Adams, PhDFulbright Postdoctoral Research Fellow Department of NeurologyMassachusetts General HospitalLunder 6 55 Fruit Street, Boston MAhttps://http://secure-web.cisco.com/1vY6vQX3fv4u-VVqRoZdHx8D66NkHui_f18x8… Medical Schoolhttps://hms.harvard.edu/ E  asorby-adams(a)mgh.harvard.edu   T +1 617 251 6465 From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of fsbuild <fsbuild@contbay.com>Date: Monday, 12 December 2022 at 15:52To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Subject: [Freesurfer] 7.3.2 release update for only Apple silicon machines (M1/M2 processors)        External Email - Use Caution        If you are running the Freesurfer 7.3.2 release on an Apple Silicon machine (M1/M2 processor) with MacOS BigSur (11.X) or Monterey (12.X) AND have seen the error message "illegal hardware instruction", then please read following.The "illegal hardware instruction" error can occur when running commands such as samseg and mri_synthseg.  This update is not necessary if your normal workflow does not include commands that produce this error.Please note the update should not be applied if:- Your Mac has an Intel processor.- Your Apple silicon machine (M1/M2 processor) is running a version of Freesurfer that is not the 7.3.2 release, e.g., a more recent development build.UPDATE PROCEDURE:You may not be able to run these commands without sudo/admin permissions on your machine.1) Download the tensorflow-2.4.1-py3-none-any.whl from,https://secure-web.cisco.com/1nk-z_nujDefDMuDjgHgXeeaRdpI0kj5fYw-uyy1X…) Check the download is OK with the md5 command in the terminal window,$ md5 tensorflow-2.4.1-py3-none-any.whlMD5 (tensorflow-2.4.1-py3-none-any.whl) = fab44de8702faf65e17a22d706a525a4DO NOT PROCEED UNTIL YOU GET THE ABOVE OUTPUT FROM the md5 command.3) Setup the Freesurfer 7.3.2 environment (shown here as installed via ..pkg file under /Applications) and verify the path to fspython is from the 7.3.2 release,$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2$ source $FREESURFER_HOME/SetUpFreeSurfer.sh-------- freesurfer-darwin-macOS-7.3.2-20220803-878457d --------... environment variable settings output ....$ which fspython/Applications/freesurfer/7.3.2/bin/fspython4) Uninstall the existing tensorflow package with,$ sudo $FREESURFER_HOME/python/bin/python3 -m pip uninstall tensorflow... apart from any warnings you should see the output ...Successfully uninstalled tensorflow-2.4.15) Install the package downloaded above.  This command assumes the package is in the current directory where the command is run.$ sudo -H $FREESURFER_HOME/python/bin/python3 -m pip install ./tensorflow-2.4.1-py3-none-any.whl... apart from warnings and output about requirements (which should all be satisfied) ...... you should see tensorflow was updated ....Successfully installed tensorflow-2.4.1CHECK THE UPDATE:$ which fspython/Applications/freesurfer/7.3.2/bin/fspython$ fspython>>> import sys, os>>> import tensorflow>>>You should see the prompt return to ">>>" after the import of tensorflow with no errors reported.  Hit Ctrl-D to escape the python session.  The update should now be complete. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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7.3.2 release update for only Apple silicon machines (M1/M2 processors)
by fsbuild 12 Dec '22

12 Dec '22

External Email - Use Caution If you are running the Freesurfer 7.3.2 release on an Apple Silicon machine (M1/M2 processor) with MacOS BigSur (11.X) or Monterey (12.X) AND have seen the error message "illegal hardware instruction", then please read following. The "illegal hardware instruction" error can occur when running commands such as samseg and mri_synthseg.  This update is not necessary if your normal workflow does not include commands that produce this error. Please note the update should not be applied if: - Your Mac has an Intel processor. - Your Apple silicon machine (M1/M2 processor) is running a version of Freesurfer that is not the 7.3.2 release, e.g., a more recent development build. UPDATE PROCEDURE: You may not be able to run these commands without sudo/admin permissions on your machine. 1) Download the tensorflow-2.4.1-py3-none-any.whl from, https://secure-web.cisco.com/18TkiXyIrlbeLHRMWJ1Sd8F-2xd8_8BiGxNMSWSbNgkohn… 2) Check the download is OK with the md5 command in the terminal window, $ md5 tensorflow-2.4.1-py3-none-any.whl MD5 (tensorflow-2.4.1-py3-none-any.whl) = fab44de8702faf65e17a22d706a525a4 DO NOT PROCEED UNTIL YOU GET THE ABOVE OUTPUT FROM the md5 command. 3) Setup the Freesurfer 7.3.2 environment (shown here as installed via .pkg file under /Applications) and verify the path to fspython is from the 7.3.2 release, $ export FREESURFER_HOME=/Applications/freesurfer/7.3.2 $ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-darwin-macOS-7.3.2-20220803-878457d -------- .... environment variable settings output ... $ which fspython /Applications/freesurfer/7.3.2/bin/fspython 4) Uninstall the existing tensorflow package with, $ sudo $FREESURFER_HOME/python/bin/python3 -m pip uninstall tensorflow .... apart from any warnings you should see the output ... Successfully uninstalled tensorflow-2.4.1 5) Install the package downloaded above.  This command assumes the package is in the current directory where the command is run. $ sudo -H $FREESURFER_HOME/python/bin/python3 -m pip install ./tensorflow-2.4.1-py3-none-any.whl .... apart from warnings and output about requirements (which should all be satisfied) ... .... you should see tensorflow was updated ... Successfully installed tensorflow-2.4.1 CHECK THE UPDATE: $ which fspython /Applications/freesurfer/7.3.2/bin/fspython $ fspython >>> import sys, os >>> import tensorflow >>> You should see the prompt return to ">>>" after the import of tensorflow with no errors reported.  Hit Ctrl-D to escape the python session.  The update should now be complete.

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numbers on color scale bar
by Kunitoki, Keiko 12 Dec '22

12 Dec '22

Hello FreeSurfer Developers, When I use Freeview color bar, the numbers displayed on the bar seem always tertiles (like -8,-2.66,2.66, 8). Is there any way we can make it quartile or edit them as we want, like the "Configure Overlay Scale Bar" function in tksurfer? Thank you, Keiko

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pass cod
by Nazanin Mirzaei 12 Dec '22

12 Dec '22

External Email - Use Caution Hello I download the FS_7_2_0_Ubuntu_18_04_06.ova.7z ,but was prompted for a password. Could I get access to this password? Best regards, Nazanin Mirzaei

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preproc-sess (AP-PA) - study design
by Asa Borzabadi Farahani 12 Dec '22

12 Dec '22

External Email - Use Caution Hi, I have two basic questions. 1- I am currently having some AP fMRI runs and I have also acquired a single PA run to be able to do distortion correction, my original plan was to use FSL and apply topup to get the undistorted fMRI data. How can I fit it within the preproc-sess command? ( I suppose the motion correction and slice timing correction should be done before topup), could you please suggest me what is more appropriate to do? 2- In my study, for each subject I did 8 runs in a single data acquisition session. The runs that I have are 2 different types; The first type of runs ( 4 runs) have black background and the other 4 runs have the gray background. My ultimate goal is to compare these 2 conditions in a group and subject level. Do you suggest that in the functional folder, I create two sessions per subject and put the four runs with gray background in session 1 and the other four runs with the black background in session 2? Thank you so much for your time and consideration. Asa Farahani Sent from Mail<https://secure-web.cisco.com/14-OsICoCS2xDYjCLpXfqNBQLlPmq6KfR6gvoFX6GyqCql…> for Windows

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Converting Volumes from Old Format to Current FreeSurfer Format
by Ngo, Nathan Xi 12 Dec '22

12 Dec '22

Hello, I have several flash volumes that I am able to open using stable5 but not with the current version of freesurfer. Is there a way to convert these volumes into the current freesurfer format? Best, Nathan

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Freesurfer