Freesurfer July 2024

freesurfer@nmr.mgh.harvard.edu

44 participants
44 discussions

Steps for Correcting Dura Using Multi-echo MPRAGE
by KEITH JONES 17 Jul '24

17 Jul '24

External Email - Use Caution Hi everyone, I am running Freesurfer on some multi-echo MPRAGE data in order to extract cortical thickness. I would like to use the multi-echo data to improve the surfaces, and I found example code to do that on a previous post. However, it's not clear to me if there are any steps after this. Do I need to rerun any part of recon-all in order to use these newly created surfaces for cortical parcellation and thickness extraction? My exact code is below: Step 1: Run recon-all recon-all -subject ${SUBJECT} -i {T1RMS} -sd ${OUTPUT} -mprage -3T -T2 ${T2} -T2pial -hires -threads 16 -all Step 2: Adjusting dura mris_make_surfaces -dura memprage_echo%d.mgz 4 -sdir ${OUTPUT} ${SUBJECT} ${HEMI} Step 3: Rerun part of recon-all to use the new surfaces? Step 4: Extract data with aparcstats2table Thanks for the help! Sincerely, Keith Jones

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mri_gtmpvc RBV - cannot find file from a custom subject directory
by Sneha Pandya 17 Jul '24

17 Jul '24

External Email - Use Caution Dear team, I am running mri_gtmpvc using RBV correction, however when I do so I get an error message saying it cannot find $SUBJECTS_DIR/$subject_id/mri/orig.mgz needed for RBV. Our Freesurfer outputs are nested as $subject_id/MPRAGE/Freesurfer/mri/orig.mgz. I tried mri_gtmpvc with "--sd" flag as well, still same error as when I set "--sd $subject_id/MPRAGE/Freesurfer" it tries to find the file as $subject_id/MPRAGE/Freesurfer/$subject_id/mri/orig.mgz. One way I can avoid doing this is by creating a soft link with the expected path, however if there is a better way to do so that would be great. Thank you, Sneha

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Maps from fsLR system (32, 492 vertices) to fsaverage5
by Stefano Delli Pizzi 14 Jul '24

14 Jul '24

External Email - Use Caution Dear, We are using the Magicc Maps (https://github.com/kwagstyl/MAGICC) The maps are in fsLR system (32,492 vertices). How can we register them in fsaverage5? Thanks Best regards Stefano

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Functional connectivity: sig.nii.gz values seem off
by Doll, Laura 12 Jul '24

12 Jul '24

External Email - Use Caution Hi, I ran a functional connectivity analysis according to the walkthrough in the Freesurfer Wiki. After the group analysis (with mri_glmfit using ces and cesvar), I plotted the results (sig.nii.gz of the GLM) with freeview, but the distribution seems off. I'll attach a screenshot, but in case someone cannot access it: There are only few negative data points, the majority seems to be in two (!) approx. gaussian distributions centered at ~5 (the smaller one) and ~8, so most points have values between 5 and 10. Running an FDR correction suggested that the threshold should be 1.3 Because the seems highly unlikely, I search the mailing list archive and found out about the bug in the functional connectivity analysis. Therefore, I repeated the group analysis with the pcc instead of the ces, but that didn't really change anything. Side note/question here: There is no variance corresponding to cesvar I could use in that case, right? Any suggestions on what could've gone wrong? Here are the exact steps I used: # Create nuisance variables for white matter: fcseed-config -wm -fcname wm.dat -fsd bold -pca -cfg wm.config fcseed-sess -sf Part3HR -cfg wm.config # Create nuisance variables for ventricles + CSF: fcseed-config -vcsf -fcname vcsf.dat -fsd bold -pca -cfg vcsf.config fcseed-sess -sf Part3HR -cfg vcsf.config # Auditory cortex ################## # configure parameters fcseed-config -roi AC-rh -fcname AC-rh.dat -fsd bold -mean -cfg AC-rh.config # create FC seeds fcseed-sess -sf Part3HR -cfg AC-rh.config # FC analysis mkanalysis-sess -analysis fc.AC.surf.rh -surface fsaverage rh -fwhm 5 -notask -taskreg AC-rh.dat 1 -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -mcextreg -polyfit 5 -nskip 4 -fsd bold -TR 2 -per-run selxavg3-sess -sf Part3HR -a fc.AC.surf.rh isxconcat-sess -sf Part3HR -analysis fc.AC.surf.rh -o AverageFC_AC -all-contrasts -map pcc mri_glmfit --y ./AverageFC_AC/fc.AC.surf.rh/AC-rh/pcc.nii.gz \ --osgm \ --surface fsaverage rh \ --glmdir ./AverageFC_AC/fc.AC.surf.rh/GLM_AC-rh \ --save-eres \ --nii.gz I'd appreciate any input. Thanks in advance! Best regards, Laura

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Doing math on mgz file
by Aaron Tanenbaum 12 Jul '24

12 Jul '24

External Email - Use Caution Is there an equivalent to fslmaths in freesurfer? Thank you

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Licence for using Freesurfer-generated images in a book?
by ALARIO Francois 12 Jul '24

12 Jul '24

External Email - Use Caution Hello I am considering using freesurfer-generated images not in a scientific paper but in a popular science book (commercial). What is the preferred course of action, license-wise, for this specific purpose? Can I include images of fsaverage with Desikan atlas parcellations, or should I avoid using fsaverage and use instead images I have acquired? The general license is worded in terms of “Software”, but said figures would not appear to laypeople to be “Software” May I skip the words "All or portions of this licensed product (such portions are the "Software") have been obtained under license from The General Hospital Corporation and are subject to the following terms and conditions:" and more plainly acknowledge that the images were created with Freesurfer by citing ''Cortical reconstruction and volumetric segmentation was performed with the Freesurfer image analysis suite, which is documented and freely available for download online (<http://surfer.nmr.mgh.harvard.edu/>)'', along with one of the papers (which one)? The book is in French the recommended option would be translated to French. Any advice would be appreciated. Kind regards Xavier -- Xavier ALARIO + 33 4 13 55 09 72 https://cv.hal.science/f-xavier-alario https://crpn.univ-amu.fr/fr/annuaire/alario-xavier

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Longitudinal Analysis Error
by Ahmet Kaya 10 Jul '24

10 Jul '24

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to perform longitudinal analysis of brain volumes with two timepoints for each patient. Some of these patients were scanned using different scanners. When creating a base file for longitudinal analysis, I encounter the following error: freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 rca-base-init 7.4.1 Darwin Kayas-MacBook-Pro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:32:11 PDT 2023; root:xnu-10002.41.9~7/RELEASE_ARM64_T6030 arm64 pid 3979 #-------------------------------------------- #@# Longitudinal Base Subject Creation Sat Jul 6 15:59:22 +03 2024 /Users/kayaacademia/Desktop/MS_LAB/10402969_base \n mri_diff --notallow-pix --notallow-geo /Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/rawavg.mgz /Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/rawavg.mgz \n error: mghRead(/Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/rawavg.mgz, -1): could not open file \n******************************************************************************* WARNING: Image parameters differ across time, maybe due to acquisition changes? Consistent changes in, e.g., resolution can potentially bias a longitudinal study! You can check image parameters by running mri_info on each input image. Will continue in 10 seconds ... *******************************************************************************\n \n mri_robust_template --mov /Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz /Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/norm.mgz --lta /Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/transforms/10402969_19_to_10402969_base.lta /Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/transforms/10402969_22_to_10402969_base.lta --template /Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/norm_template.mgz --average 1 --sat 4.685 \n 7.4.1 --mov: Using /Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz as movable/source volume. --mov: Using /Users/kayaacademia/Desktop/MS_LAB/10402969_22/mri/norm.mgz as movable/source volume. Total: 2 input volumes --lta: Will output LTA transforms --template: Using /Users/kayaacademia/Desktop/MS_LAB/10402969_base/mri/norm_template.mgz as template output volume. --average: Using method 1 for template computation. --sat: Using saturation 4.685 in M-estimator! reading source '/Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz'... error: mghRead(/Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz, -1): could not open file error: MultiRegistration::loadMovables: could not open input volume /Users/kayaacademia/Desktop/MS_LAB/10402969_19/mri/norm.mgz. ERROR: Darwin Kayas-MacBook-Pro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:32:11 PDT 2023; root:xnu-10002.41.9~7/RELEASE_ARM64_T6030 arm64 recon-all -s 10402969_base exited with ERRORS at Sat Jul 6 15:59:33 +03 2024 I have attached the recon-all.log file for your reference. I am not a data scientist and am unable to determine the cause of this issue. I would greatly appreciate your guidance on how to resolve this error. 1. *FreeSurfer version:* freesurfer-macOS-darwin_x86_64-7.4.1-20230614-7eb8460 2. *Platform:* macOS 23.1.0 3. *uname -a:* Darwin Kayas-MacBook-Pro.local 23.1.0 Darwin Kernel Version 23.1.0: Mon Oct 9 21:32:11 PDT 2023; root .41.9~7/RELEASE_ARM64_T6030 arm64 4. *recon-all.log:* see attached Thank you for your assistance, much appreciated. Best regards, Ahmet Kaya, MD

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BUG: FTP Server data visible without credential
by Kavar Hardik 10 Jul '24

10 Jul '24

External Email - Use Caution Hello FreeSurfer Developers, I am checking your website and I found your FTP server are configured without Credentials. FTP URL: https://surfer.nmr.mgh.harvard.edu/ftp/ POC attached with mail. Regards Kavar Hardik

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Unknown recon-all error - ERROR: reading ../surf/autodet.gw.stats.lh.dat
by Austin Cooper 09 Jul '24

09 Jul '24

External Email - Use Caution Hello there! I'm hoping that someone can resolve this issue which I'm having. To me it seems that the pipeline is looking for ../surf/autodet.gw.stats.lh.dat, and I can confirm that it does not exist. Is there a quick solution? Everything in recon-all was functioning without error up to this point. The error is as follows: mri_vol2vol done #-------------------------------------------- #@# c2hWhiteSurfs lh Thu Jul 4 23:07:31 EDT 2024 cd /project/6001995/Shmuel_Mendola/data/MGH/HCPNaming/control/05_scan1/T1w/05/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg rawavg.aseg.presurf.mgz --wm rawavg.wm.mgz --invol rawavg.brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc.rawavg --o ../surf/lh.white.rawavg --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-wmsa --rip-surf ../surf/lh.white.preaparc.rawavg --aparc ../label/lh.aparc.annot ERROR: reading ../surf/autodet.gw.stats.lh.dat ERROR: Linux bc11246.int.ets1.calculquebec.ca 4.18.0-513.24.1.el8_9.x86_64 #1 SMP Thu Apr 4 18:13:02 UTC 2024 x86_64 GNU/Linux recon-all -s 05 exited with ERRORS at Thu Jul 4 23:07:32 EDT 2024 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Yours truly, Austin Cooper BEng - University of Guelph PBD - Cognitive Science - Carleton University PhD Candidate - Neuroscience - McGill University

2 1

LME model error: mris_average_surface failed
by Bondi, Daniel 09 Jul '24

09 Jul '24

External Email - Use Caution Hello, I am trying to test the LME model created by Bernal using mass-univariate data. Although my entire dataset has about 40 participants with pre- and post-season scans, I am trying to test the pipeline with the data from one subject. On my Mac, I am unable to run “make_average_subject” for the test subject successfully without error. The error message is “ERROR: creating directory / mri_average_surface failed”. Freesurfer is able to create a directory within the subject folder on my desktop (study_average) but can’t make a “surf” folder within that. When I run sudo before this command, the error is “FREESURFER_HOME: undefined variable” even though I have it defined in my bash profile and echoing it shows /Applications/freesurfer/7.3.2. I was on Freesurfer 7.2.0 originally, but I’ve now upgraded to 7.3.2 to fix this error but had no luck. I’ve also changed all the read/write permissions in the file directories but still no luck. Thanks, Daniel

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