Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30066 discussions

freesurfer data analysis and visualization
by Pukovisa Prawiroharjo 10 Sep '23

10 Sep '23

External Email - Use Caution anyone have suggestion data visualization from freesurfer volumetric. i need visualization of 2 volume before and after of the same individual patient and between 2 groups in a research. i've found some paper use pysurfer, anyone have other suggestions and tutorioal / reading and code about how to use those ? best regards *Pukovisa Prawiroharjo, M.D., Sp.N, Subsp. NGD (K), PhD* Neurobehavior Consultant, Neurology Specialist Neurology Department, Faculty of Medicine, Universitas Indonesia Chair of Bioethics Cluster IMERI UI Chair of International Policy Div, Board of Development Med Services IDI

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keep T1w matrix size during recon-all (without zero-padding)
by Rona Haker 10 Sep '23

10 Sep '23

External Email - Use Caution Hi, Can recon-all be performed without zero-padding the final matrix aparc+aseg in order to keep the original T1w matrix size? This will greatly help me in further analyses. Thank you!

2 1

GLM with multiple nuisance variables
by #NGUYEN THUAN TINH# 10 Sep '23

10 Sep '23

External Email - Use Caution Dear Freesurfer experts, I want to run a GLM to analyze the correlation between a continuous variable Y and a morphometric measure (eg. Cortical thickness). I want to control for some nuisance variables: sex, scan site, age, age squared, age * sex interaction, head size. 1. How should I go about formulating the FSDG file? 2. What should my design matrix be if I am only interested in the relationship between Y and the morphometric measure of interest after controlling for the various nuisance variables? Thank you so much for the help! Yours, Sophia

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SAMSEG choice of the input
by Giulio Siracusano 10 Sep '23

10 Sep '23

External Email - Use Caution Dear Experts, I'm trying to understand what is the best input choice for running SAMSEG --recon in order to have the closest results as possible when compared against ASEG after executing (separately) an instance of recon-all all (and the raw input files in NIFTI format). I'm very well aware that ASEG and SAMSEG are different methods. I'm using the aseg.stats file as a results of the recon-all all command (here renamed as aseg.recon-all.stats for an easier identification). These stats should be my reference. Currently I've run the samseg command using the following input variants: 1) raw input file (brain MP-RAGE sequence) converted into a mgz archive (Raw.mgz). samseg --t1w ./Raw.mgz --s 002_S_0685_DIRECT --recon --refmode t1w The corresponding results are attached into (samseg.direct.stats) 2) This time I've used the file T1.mgz which is one of the intermediate results generated after running recon-all -autorecon 1. Specifically, this is the output of (mri_normalize <https://secure-web.cisco.com/1JV3nYNrViePm1qpOtzuMUtCndnVtCut-gp7OyXxNuXIOk…> -g 1 -mprage nu.mgz T1.mgz). samseg --t1w ./T1W/T1.mgz --s 002_S_0685_DIRECT_T1W --recon --refmode t1w The corresponding samseg.stats file is attached and called (samseg.direct.t1.stats). 3) this time I've used the file brainmask.mgz which is the last intermediate result generated after running recon-all -autorecon 1. Specifically, this is the output of mri_watershed <https://secure-web.cisco.com/1DjG5BDGTEbHYOWKmd4lc63SOmX8IrmziV9_NRWhpCskwO…>. samseg --t1w ./brainmask.mgz --s 002_S_0685_DIRECT_BRAIN --recon --refmode t1w The corresponding samseg.stats file is attached and called (samseg.brain.stats). I've noticed that the SAMSEG stats file (samseg.brain.stats) as obtained when using the brainmask.mgz as input file is the closest with the ASEG statistics (aseg.recon-all.stats). I also observe that the unknown volume is the lowest (# Measure Unknown, 5329.102436, mm^3) when using brainmask.mgz as input for SAMSEG, whereas is higher (Measure Unknown, 325302.894793, mm^3) when using T1.mgz as input file and is the highest (Measure Unknown, 946924.354060, mm^3) for the raw input. I know that for running recon-all we use the raw input files (for example, in NIFTI format), but I wanted to know what is the best possible configuration for SAMSEG in terms of input file in order to have the closest match between SAMSEG and ASEG statistics. Could it be possible to use the intermediate result T1.mgz or brainmask.mgz as input file for running samseg command? Is it a technically correct procedure? Do we need to use only the raw data as input for running samseg --recon command? Hope this is clear Regards GS

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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

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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

1 0

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]

1 0

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

1 0

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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Freesurfer