Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30061 discussions

Re: [Freesurfer] Screen tearing in FreeView on Ubuntu 22.04
by fsbuild 07 Sep '23

07 Sep '23

External Email - Use Caution I’ll suggest a couple of things - (1) you are using a development build of freesurfer which could be unstable.  I would instead try the most recent 7.4.1 release for Ubuntu, and install it via the .deb file installer (system updates may be needed), which you can pick from the downloads available under https://secure-web.cisco.com/1lN9y7zM2gRNbX1ihQ-zCX4n48mKFb2WobA…  Just “sudo apt remove freesurfer” and then “sudo apt install ./<freesurfer deb file>”.  (2)  Perhaps something is going on with OpenGL drivers and graphics hardware.  You could check the latest OpenGL drivers are installed and what you are running is compatible with your version of Ubuntu Linux. - R. On Sep 7, 2023, at 19:40, VINCENT KOPPELMANS <vincent.koppelmans@utah..edu> wrote:        External Email - Use Caution        Hi all, I am encountering the following issue: In FreeView, when I use the mouse to navigate, the crosshair is not under the cursor, but about an inch left and down from it. When I resize the FreeView window, it starts to tear. See the attached screenshot or the Github issue that I opened here: https://secure-web.cisco.com/1nxOyRuDDwSL9nzRXpr6kl-rtPsHnh83mO2… environment:OS: Ubuntu 22.04.3 LTS (but this happened with 20.04 as well)FreeSurfer: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460FreeView: 3.0; Build Jun 14 2023 03:48:54 (but this happened with previous versions as well)Best,Vincent<261422837-033513d0-3922-4a07-95fe-ff30357b5085.png>_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh..harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Screen tearing in FreeView on Ubuntu 22.04
by VINCENT KOPPELMANS 07 Sep '23

07 Sep '23

External Email - Use Caution Hi all, I am encountering the following issue: In FreeView, when I use the mouse to navigate, the crosshair is not under the cursor, but about an inch left and down from it. When I resize the FreeView window, it starts to tear. See the attached screenshot or the Github issue that I opened here: https://secure-web.cisco.com/1SmkQJ514wrbsEV9WUJ5prR-A5a9dCAvuoTt6R1xbFtDV-… My environment: OS: Ubuntu 22.04.3 LTS (but this happened with 20.04 as well) FreeSurfer: freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 FreeView: 3.0; Build Jun 14 2023 03:48:54 (but this happened with previous versions as well) Best, Vincent [cid:d15c4131-9aec-4fcc-b8b2-ba224c9ce0e6]

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visualizing a tract and a ROI
by Zeng, Qi 07 Sep '23

07 Sep '23

External Email - Use Caution Hi, I was trying to demonstrate my findings by visualizing a significant tract and a ROI at the same time on a single template or volume, for example, left UNC and orbitofrontal overlaid on the T1-weighted.nii. However, I only saw Freeview on tractography using -v and on surface using -f separately. Is there a way to achieve this? If not, do you have any suggestions for tools to use for visualizing a tract and ROI simultaneously? Additionally, may I know which atlas is used for TRACULA and where I can download both the 18 and 42 white matter tract atlases? Thank you so much! Best, QZ

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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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FreeSurfer hippo-amygala module
by Dr. Anton Jakovcic 06 Sep '23

06 Sep '23

External Email - Use Caution Dear all, here is Anton - a PhD candidate from Max Planck Institute for Human Cognitive and Brain Research in Leipzig, Germany. Using FreeSurfer module segment_subregions, I successfully segmented amygdala for individual HCP subjects. Thanks a lot for developing it! Currently, I am trying to get a group-level or a MNI-level segmentation to build a representative figure. Do you think, is it possible to segment amygdala in MNI-registration template? Any help/suggestion is appreciated. Kind regards Anton Jakovcic

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Re: [Freesurfer] converting preprocessed surface functional data to volume
by wangzhiwei3233 06 Sep '23

06 Sep '23

External Email - Use Caution Dear Doug, Thank you for your replying. I collected the data by myself using a SIEMENS machine. Sorry, what do you mean by mapping the time course. I guess I am not trying to do that. I would like to do beta series analysis. I used the command in its old way, and I mapped it to 2mm template. It is OK now. The time and space are both acceptable. The code is as follows, I will really appricate it if you can help me to check the code. mri_surf2vol --hemi ${hemi} --o ${ROOTDIR}/$isub/bold/${irun}/spmRibbon${hemi}/${iVolume} --projfrac 0 --fillribbon --template ${SUBJECTS_DIR}/fsaverage/mri.2mm/brain.mgz \ --reg ${SUBJECTS_DIR}/fsaverage/mri.2mm/reg.2mm.dat --surfval ${ROOTDIR}/$isub/bold/${irun}/spm${hemi}/${iVolume} Best, Zhiwei >Message: 5 >Date: Sun, 20 Aug 2023 17:23:52 -0400 >From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> >Subject: Re: [Freesurfer] converting preprocessed surface functional > data to volume >To: freesurfer(a)nmr.mgh.harvard.edu >Message-ID: <c31ec38b-fcd6-c47a-8b29-f32857181a0f(a)mgh.harvard.edu> >Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > >where did the functional data come from? Are you trying to map the time >courses? That usually does not work that well as your resulting image >will be huge. One thing to do is to map it to a cropped volume (most of >the 256^3 is outside the brain) and or also map it to 2mm instead of 1mm. > >On 8/13/2023 11:02 PM, wangzhiwei3233 wrote: >> >> ????????External Email - Use Caution >> >> Dear Freesurfer experts, >> I am going to convert the preprocessed surface functional data to >> volume in fsaverage space so that I can used the processed data in SPM >> for further analysis, for example, beta series analysis. I tried >> mri_surf2vol, it worked. But it is time consuming. It takes around 5 >> minutes per 10 volumes. In addition, the result volume is too big >> (67MB/ volume for 256*256*256 matrix, 1mm resolution). My data >> contains about??70800 brain volumes, so the needed time is about >> 40days and the storage space is about 7TB , which is unacceptable. The >> code is? as follows: >> >> /mri_surf2vol --o >> ${Dir_Subj_fMRI}/$isub/bold/${irun}/Ribbon/${iVolume} --subject >> fsaverage --so ${SUBJECTS_DIR}/fsaverage/surf/lh.white >> ${Dir_Subj_fMRI}/$isub/bold/${irun}/LH/${iVolume} --so >> ${SUBJECTS_DIR}/fsaverage/surf/rh.white >> ${Dir_Subj_fMRI}/$isub/bold/${irun}/RH/${iVolume} / >> / >> / >> Are there methods with faster speed and outputing volumes with lower >> resolution? >> >> Best, >> Zhiwei

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registration error (reCAPTCHA not checked)
by lizhao_du＠sjtu.edu.cn 06 Sep '23

06 Sep '23

External Email - Use Caution Hi there, I am Oscar. Recently I am using FreeSurfer for fMRI data analysis. A license is required yet I could not get the license.txt from my e-mail. After filling the form from https://secure-web.cisco.com/174jctt4T-x9hrxRO4K0cJXM-oWXh3mvxRN7Dqptum9XXF…, a registration error occured (see below). Is there something wrong for my internet? Or what could I do to get the license? A few words from you may help me a lot. Thanks in advance. Best! Lizhao Du School of Biomedical Engineering, Shanghai Jiao Tong University Lizhao_Du(a)sjtu.edu.cn

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Re: [Freesurfer] Voxel co-ordinates under pial surface patch
by Alastair Snell 05 Sep '23

05 Sep '23

External Email - Use Caution Hi Yujing, Thanks for the reply. That's correct, I received an annotation file from running 'mris_find_flat_regions -t 0.99 -s 20 <input file> <output file>'. If I'm not mistaken, it seems that mri_annotations2label would output labels which correspond to the same surface as the annotation; I would like to achieve a label file pertaining to the volume of cortex immediately underneath the flat patch of pial surface for which I have an annotation file. I hope this makes sense and any help from anyone is really appreciated. Thanks, Alastair

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Re: [Freesurfer] MATLAB autorecon3 glibc error
by fsbuild 05 Sep '23

05 Sep '23

External Email - Use Caution  If you have not already done so, I would try installing and running a version of the Matlab runtime environment (which is not a full blown Matlab installation) that freesurfer was tested with.  For the 7.4.1 freesurfer release, that should be R2019b.  (Prior to that, it was R2014b - which you could try as well - but that would likely contain an even older version of glibc). Assuming that you can write to your own installed version of freesurfer, then once you have set FREESURFER_HOME, you can try running the fs_install_mcr script included with the freesurfer distribution.  See bash shell commands below. - R. $ 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 any references to your previous matlab 2020a environment from PATH, LD_LIBRARY_PATH, etc.  - R.

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MATLAB autorecon3 glibc error
by Paulk, Angelique C.,PhD 05 Sep '23

05 Sep '23

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to run recon-all, whether the full recon or a part of the process (e.g. recon-all -autorecon3 -s $SUBJECT -localGI) and am finding there would be what seems to be a glibc error (e.g. https://secure-web.cisco.com/1aJXVSDwcefv7rhlrTYwyBgTiVEvYt2dSphBaETv3j1Zle…) that occurs during any one of the MATLAB steps of the recon-all process. Certain versions of MATLAB appear to be missing the correct installations for glibc so I did follow the steps to install it (e.g. https://secure-web.cisco.com/1Zt0UN3L2lns-RzoRlpw4wwob_uSJBgC8w5Pk-IdqY6Mvb… ), but this error has been wildly inconsistent. For instance, the challenging issue is that this Freesurfer installation appears to work perfectly fine for some cases but would error out (one example set of errors below) causing me to think it is the glibc issue. Further, it is not consistent which MATLAB-based step causes the error (it could error out in one of the many MATLAB steps for one brain scan but it would be a different MATLAB step for another brain scan). Therefore, I have multiple error-ed out recon-all files across 15 scans (different participants) which all appear to stop at different stages of the process. Error example: MATLAB is selecting SOFTWARE OPENGL rendering. Inconsistency detected by ld.so: ../elf/dl-tls.c: 481: _dl_allocate_tls_init: Assertion `listp->slotinfo[cnt].gen <= GL(dl_tls_generation)' failed! ERROR: find_corresponding_center_FSformat did not complete successfully! Command exited with non-zero status 1 @#@FSTIME 2023:09:04:18:17:29 mris_compute_lgi N 2 e 17.45 S 4.32 U 44.58 P 280% M 2246188 F 0 R 1909235 W 0 c 909 w 36844 I 0 O 39440 L 1.01 1.06 1.07 @#@FSLOADPOST 2023:09:04:18:17:47 mris_compute_lgi N 2 1.74 1.22 1.13 Linux ebonyandrgb 5.4.0-137-generic #154~18.04.1-Ubuntu SMP Tue Jan 10 16:58:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux recon-all -s XXXXXX_SurferOutput exited with ERRORS at Mon Sep 4 18:17:47 EDT 2023 I've searched the list and no similar errors have been reported for recent MATLAB installations. Does anyone have any thoughts on how to trouble-shoot this one? I can send the recon-all log as well if need be though there are a number of them. 1) FreeSurfer version: freesurfer-linux-ubuntu18_amd64-7.4.1 2) Platform: Ubuntu 18 3) uname -a: Linux ebonyandrgb 5.4.0-137-generic #154~18.04.1-Ubuntu SMP Tue Jan 10 16:58:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: Can send following deidentification if need be but there are multiple examples of recon-all.log errors 5) MATLAB 2020a

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