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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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missing values, aseg
by Eszter Boros 12 Dec '22

12 Dec '22

External Email - Use Caution Dear FreeSurfer Team, I am writing because I was extracting the aseg values using Freesurfer 7.1.1 and much to my surprise, these values were 'empty', or zero: 5th-Ventricle WM-hypointensities Left-WM-hypointensities Right-WM-hypointensities non-WM-hypointensities Left-non-WM-hypointensities Right-non-WM-hypointensities What could be the reason behind this? How can I get these values? I used the following command: asegstats2table --subjects subject1 subject2 (... etc) --common-segs --meas volume --stats=aseg.stats --table=aseg.volume.txt Thank you for your help in advance! And let me know if you need any more information. All the best, Eszter Boros

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Fusion of PET and T1 weighted
by Amar Shukla 12 Dec '22

12 Dec '22

External Email - Use Caution Dear Freesurfer Community. I want to do image fusion (PET+T1) = T' weighted image. Then I want to go for the feature extraction from this T1 modality which I will get from the fusion.So how i can go for this. Questions are: 1) Do I have to use PET Surfer for this? Does Pet Surfer support the fusion of the two different modality. 2) I am in the perception that I want PET+ T = T' , or does it justify the multimodality approach for the detection of disease. 3) If i extract features from the different modality and then i combine it. Can we say that this is the multimodality approach of Image Fusion. Please advise me and provide the approach or the tool which will help me for the multimodality. -- With Regards, Amar Shukla Assistant Professor, M tech AI ANN(2014-2016), Centre Of Information Technology, UPES Contact :+91 897 977 8016

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FreeSurfer equivalent to fslsplit?
by Wighton, Paul 12 Dec '22

12 Dec '22

Hey FreeSurfer aficionados, Is there a FreeSurfer equivalent to fslsplit? If I have a 4d nifti, is there a way to split that into a set of 3d niftis from the command line? Thanks, -Paul

3 3

outputs for recon-all of T1-weighted and intersubject registration
by Zeng, Qi 12 Dec '22

12 Dec '22

External Email - Use Caution Hi Freesurfer experts, If I just want to normalize, register, and segment the T1-weighted images to the GM, WM, and CSF tissues, can certain steps be skipped from recon-all, such as the inflation process? What is the output for the segmentation of GM, WM, and CSF tissues? is aseg.mgz or aparc+aseg.mgz better? Following that, if I want to apply an affine transformation for all subjects to a common template, is the following command line correct? > mri_convert aparc+aseg.mgz aparc+aseg.nii.gz > bet aparc+aseg.nii.gz my_structural.nii.gz > flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in my_structural.nii.gz -omat my_affine_transf.mat > fnirt --in=aparc+aseg.nii.gz --aff=my_affine_transf.mat --cout=my_nonlinear_transf --config=T1_2_MNI152_2mm > applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=aparc+aseg.nii.gz --warp=my_nonlinear_transf --out=my_warped_structural Best, QZ

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