Freesurfer August 2023

freesurfer@nmr.mgh.harvard.edu

89 participants
126 discussions

Copy geometry (fov position) from one header to another while keeping voxel and matrix sizes unchanged
by Proulx, Jean Sebastien 08 Sep '23

08 Sep '23

External Email - Use Caution Dear Freesurfers! I have two single-slice images that were acquired with different head positions. Thanks to a fancy AutoAlign-like routine at the scanner (areg by Paul Wighton), the fov of the second image tracked the movement of the head—the brain nicely aligns when overlaying the two untouched image grids with e.g. fslview. To leverage this online registration and properly visualize images in freeview, I need the fov position in header of the second image to be the same as in the header of the first image—basically pretending the head did not move and the two images were acquired with the exact same scanner-space fov position. So far I achieved that in a somewhat inelegant way by loading the first header in matlab with MRIread.m and manually adding the volume data from the second image before saving with MRIwrite.m. That however does not work when the second image have different voxel and matrix sizes—e.g. my second image has twice the resolution of the first and gets blown up to twice the size in freeview after my makeshift header change :-( I suspect a better solution could use mri_vol2vol with an appropriate registration matrix, but I don't know how to get the appropriate matrix. Any suggestions? thanks a lot for the help and Have a very good day! Sébastien

4 7

T2 FLAIR Images
by Alan Francis 07 Sep '23

07 Sep '23

External Email - Use Caution Good evening Doug et all: I am trying to coregister T1 and T2 images and run the recons. However, the T2's are giving me an error message. Please see below: I opened the T2 image on Freeview. It looks normal. I tried running a second brain. Same problem. Appears normal on Freeview but recons wont run. So I tried running the recons on the T1 alone and it ran without problems. Thanks, Alan [DMK6P4G6FJ1G:~/SUBJECTS] alanfrancis% recon-all -all -subjid NCANDA_S00042/ fs-check-version --s NCANDA_S00042 --o /var/folders/z4/3sg7yzm101vbwnsmzcdx70n40000gq/T//tmp.W6p7a1 Mon Aug 7 16:06:21 CDT 2023 setenv SUBJECTS_DIR /Users/alanfrancis/SUBJECTS cd /Users/alanfrancis/SUBJECTS /Applications/freesurfer/7.4.1/bin/fs-check-version --s NCANDA_S00042 --o /var/folders/z4/3sg7yzm101vbwnsmzcdx70n40000gq/T//tmp.W6p7a1 -rwxrwxr-x@ 1 alanfrancis faculty 18565 Jun 13 23:24 /Applications/freesurfer/7.4.1/bin/fs-check-version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 $Id$ Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 pid 9192 Current FS Version freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 Subject does not have a bstampfile, copying /Applications/freesurfer/7.4.1/build-stamp.txt Subject FS Version: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 No constraints on version because REQ=UnSet and FsVerFile=NotThere #@#% fs-check-version match = 1 fs-check-version Done INFO: SUBJECTS_DIR is /Users/alanfrancis/SUBJECTS Actual FREESURFER_HOME /Applications/freesurfer/7.4.1 Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 #-------------------------------------------- #@# MotionCor Mon Aug 7 16:06:22 CDT 2023 Found 2 runs /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #----------------------------------------------- /Users/alanfrancis/SUBJECTS/NCANDA_S00042 \n mri_robust_template --mov /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz --average 1 --template /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001-iscale.txt /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002-iscale.txt --subsample 200 --lta /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.lta /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.lta \n 7.4.1 --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz as movable/source volume. --mov: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enabling intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz'... converting source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz'... converting source '/Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 0.4688, 0.4688, 0.6 size(0) = 0.9375, 0.9375, 1.2 *error: MultiRegistration::loadMovables: voxel size is different /Users/alanfrancis/SUBJECTS/NCANDA_S00042/mri/orig/002.mgz.* Darwin DMK6P4G6FJ1G 22.6.0 Darwin Kernel Version 22.6.0: Wed Jul 5 22:21:53 PDT 2023; root:xnu-8796.141.3~6/RELEASE_ARM64_T6020 arm64 recon-all -s NCANDA_S00042 exited with ERRORS at Mon Aug 7 16:06:29 CDT 2023

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Error mri_ca_register
by Shamas, Mohamad 01 Sep '23

01 Sep '23

External Email - Use Caution Hello, I am having a problem running Freesurfer on Linux server Centos 7. I installed freesurfer correctly and when I try to run the command: recon -all -s sample -I sample-001.mgz -all I get an error message : mri_ca_register with non-zero status 9 I attached here the log file, I am using version 7.4.1. Can you please help me figure out a solution for the problem. Thanks MShamas ________________________________ UCLA HEALTH SCIENCES IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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passcode
by Alex Gomez 31 Aug '23

31 Aug '23

External Email - Use Caution Hi, I would like to request the passcode for unzipping the Virtual Box Image file (i.e. FS_7_2_0_ubuntu_18_04_06.ova.7z). Best regards Alex

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Fwd: recon-all error: matlab gives: Unrecognized function or variable 'make_outer_surface'.
by fsbuild 30 Aug '23

30 Aug '23

External Email - Use Caution If you have not already done so, I would try installing and using the newest version of the Matlab runtime environment that the 7.4.1 release was tested with, i.e. R2019b.  Once you have set $FREESURFER_HOME, then run the fs_install_mcr script included with the freesurfer distribution .... $ export FREESURFER_HOME=<your install path> $ cd $FREESURFER_HOME/bin $ sudo FREESURFER_HOME=$FREESURFER_HOME  ./fs_install_mcr  R2019b … answer y to any installer questions ... Then I think it should work to find the Matlab libraries by at least start off with setting, $ export LD_LIBRARY_PATH=$FREESURFER_HOME/MCRv97/bin/glnxa64 Please make sure you have otherwise removed from your environment and references to the previous Matlab R2022b setup. - R. Begin forwarded message:From: Benjamin Cole Sherman <bsherma(a)stanford.edu> Subject: [Freesurfer] recon-all error: matlab gives: Unrecognized function or variable 'make_outer_surface'. Date: August 30, 2023 at 12:02:09 EDT To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu>         External Email - Use Caution        Hi FreeSurfer Team,I'm trying to run recon-all on an MRI nii.gz file and I believe most of the command runs as the error doesn't happen until several hours in, however once matlab is initiated I consistently get the following output:MATLAB is selecting SOFTWARE OPENGL rendering.                            < M A T L A B (R) >                  Copyright 1984-2022 The MathWorks, Inc.                  R2022b (9.13.0.2049777) 64-bit (glnxa64)                              August 24, 2022Warning: Function iscolumn has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict.Warning: Function ismatrix has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict.Warning: Function isrow has the same name as a MATLAB builtin. We suggest yourename the function to avoid a potential name conflict.Warning: Function narginchk has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict.Warning: Function isequaln has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict.Warning: Function istable has the same name as a MATLAB builtin. We suggest yourename the function to avoid a potential name conflict.Warning: Function isfile has the same name as a MATLAB builtin. We suggest yourename the function to avoid a potential name conflict.Warning: Function isfolder has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict..Warning: Function isstring has the same name as a MATLAB builtin. We suggestyou rename the function to avoid a potential name conflict. For online documentation, see https://secure-web.cisco.com/1A7cHJG7OTQToCpTNsg3ycqt5UEObzYbnyuy3… product information, visit http://secure-web.cisco.com/1PkNE_zNSBM0yzYMjwH_cGeVC4O7UdJdfnli… Unrecognized function or variable 'make_outer_surface'. >> ERROR: make_outer_surface did not create output file '/usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!Command exited with non-zero status 1I haven't been able to find anything in the support archives so I was hoping you could help us out.1)Freesurfer version: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb84602)Platform: Ubuntu 20.04.6 LTS3)recon-all.log: see attachedThanks for any help you can provide!_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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recon-all error: matlab gives: Unrecognized function or variable 'make_outer_surface'.
by Benjamin Cole Sherman 30 Aug '23

30 Aug '23

External Email - Use Caution Hi FreeSurfer Team, I'm trying to run recon-all on an MRI nii.gz file and I believe most of the command runs as the error doesn't happen until several hours in, however once matlab is initiated I consistently get the following output: MATLAB is selecting SOFTWARE OPENGL rendering. < M A T L A B (R) > Copyright 1984-2022 The MathWorks, Inc. R2022b (9.13.0.2049777) 64-bit (glnxa64) August 24, 2022 Warning: Function iscolumn has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function ismatrix has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function isrow has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function narginchk has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function isequaln has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function istable has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function isfile has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function isfolder has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. Warning: Function isstring has the same name as a MATLAB builtin. We suggest you rename the function to avoid a potential name conflict. For online documentation, see https://secure-web.cisco.com/13dZgITxzA846nUba6W_D2_W9PFkrs3ibHMRaWbFXiq0_q… For product information, visit http://secure-web.cisco.com/1wgw042nbZL0hU6HIRu6Xfp7twuvdIG8MKHiB4v2D5d-qKz… >> Unrecognized function or variable 'make_outer_surface'. >> ERROR: make_outer_surface did not create output file '/usr/local/freesurfer/7.4.1/subjects/EP01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Command exited with non-zero status 1 I haven't been able to find anything in the support archives so I was hoping you could help us out. 1)Freesurfer version: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 2)Platform: Ubuntu 20.04.6 LTS 3)recon-all.log: see attached Thanks for any help you can provide!

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Converting hyperfine MRI to nifti
by Fatima Karim 29 Aug '23

29 Aug '23

External Email - Use Caution Hello My lab is trying to analyze hyperfine acquired MRI using freesurfer. We are stuck at the step where freesurfer converts the dicom to nifti for analysis. Freesurfer cannot recognize the hyperfine as a manufacturer and exiting with this error. Can you please share the script you used to analyze hyperfine images starting from conversion till the end with me? Best Fatima Get Outlook for Android <https://secure-web.cisco.com/16jfFKrMp4E5uGCHCwQmLcL0M2XuJLc2D1i3F2Ezs1kUcA…>

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Password for extracting VM files
by TISSOT Ugo (NCPS) 29 Aug '23

29 Aug '23

External Email - Use Caution Hello, I am going through the installation of Freesurfer with VM and Ubuntu, could you provide me the password needed to finish it? Best regards, U.T

1 0

[FreeSurfer] ValueError axes don't match array
by Cerri, Stefano,PHD 29 Aug '23

29 Aug '23

External Email - Use Caution Hi Krystal, Can you send your samseg command and the output of mri_info on both the T1 and coregistered FLAIR images? It seems that the two images have different image sizes. Stefano Subject: [Freesurfer] [FreeSurfer] ValueError axes don't match array Date: Tue, 22 Aug 2023 04:22:09 +0000 From: Krystal Xiwing Yau <krystaly(a)hku.hk><mailto:krystaly@hku.hk> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> External Email - Use Caution Dear FreeSurfer experts, I have completed the processes of coregistration of FLAIR to T1 image for the subject. As I ran samseg with lesion contrast, the following error message occurred: writing template transform to /home/admin1/freesurfer/subjects/103_samsegOutput/template.lta writing talairach transform to /home/admin1/freesurfer/subjects/103_samsegOutput/samseg.talairach.lta atlas registration complete: 0:00:17.614971 /home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/_asarray.py:83: VisibleDeprecationWarning: Creating an ndarray from ragged nested sequences (which is a list-or-tuple of lists-or-tuples-or ndarrays with different lengths or shapes) is deprecated. If you meant to do this, you must specify 'dtype=object' when creating the ndarray return array(a, dtype, copy=False, order=order) Traceback (most recent call last): File "/home/admin1/freesurfer/python/scripts/run_samseg", line 190, in <module> _, _, _, optimizationSummary = samseg.segment( File "/home/admin1/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 255, in segment self.preProcess() File "/home/admin1/freesurfer/python/packages/freesurfer/samseg/Samseg.py", line 318, in preProcess self.imageBuffers, self.transform, self.voxelSpacing, self.cropping = readCroppedImages( File "/home/admin1/freesurfer/python/packages/freesurfer/samseg/SamsegUtility.py", line 139, in readCroppedImages croppedImageBuffers = np.transpose(croppedImageBuffers, axes=[1, 2, 3, 0]) File "<__array_function__ internals>", line 5, in transpose File "/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 653, in transpose return _wrapfunc(a, 'transpose', axes) File "/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 55, in _wrapfunc return _wrapit(obj, method, *args, **kwds) File "/home/admin1/freesurfer/python/lib/python3.8/site-packages/numpy/core/fromnumeric.py", line 44, in _wrapit result = getattr(asarray(obj), method)(*args, **kwds) ValueError: axes don't match array Would somebody be kindly advise? Thank you. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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Freesurfer Windows instalation
by Dominika Życka 29 Aug '23

29 Aug '23

External Email - Use Caution Hi, I'm having trouble installing Freesurfer on Windows. I want to use Virtual Machine to open FS_7_2_0_Ubuntu_18_04_06.ova.7z file. Could I get the password for this file please? Freesurfer would be very useful in my research on the analysis of brain symmetry in neurodegenerative and neuropsychiatric diseases. Best regards, Dominika Życka-Malesa Warsaw University of Technology, Faculty of Mathematics and Information Science

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Freesurfer August 2023