Freesurfer December 2024

freesurfer@nmr.mgh.harvard.edu

45 participants
62 discussions

surfreg error: typo in mris_convert command
by Suzanne Witt 03 Dec '24

03 Dec '24

External Email - Use Caution Hello, I recently updated to Freesurfer 7.4.1 (previously running 7.2.0) and am trying to get my full workflow to run. I am getting the following error when I try to run “surfreg –s test –t fsaverage_sym –lh –xhemi –no-annot”: #CMD# mris_convert --center --vol-geom /usr/local/freesurfer/subjets/fsaverage/mri/orig.mgz /usr/local/freesurfer/subjects/test/xhemi/surf/lh.fsaverage_sym.sphere.reg /usr/local/freesurfer/subjects/test/xhemi/surf/lh.fsaverage_sym.sphere.reg centering surface error: mghRead(/usr/local/freesurfer/subjets/fsaverage/mri/orig.mgz, -1): could not open file It looks as if there is a typo in the path to “orig.mgz”, where “freesurfer/subjets” should be “freesurfer/subjects”. I’ve not found anything searching for “surfreg” in the message board that points to a corrected surfreg binary. 1. Freesurfer version: freesurfer-linux-ubuntu20_x86_64-7.4.1-20230614-7eb8460 2. Platform: python:3.9-debian Docker image 3. uname -a: Linux 828abe00572a 6.5.0-1024-gcp #26~22.04.1-Ubuntu SMP Fri Jun 14 18:48:45 UTC 2024 x86_64 GNU/Linux 4. Full terminal dump attached Thanks and cheers. Suzanne T. Witt, PhD Scientific Solutions Engineer suzannewitt(a)flywheel.io<mailto:suzannewitt@flywheel.io> she/her flywheel.io<https://secure-web.cisco.com/1EXwUbHzeZQUocP35tQvPjHOZdzbGXFKv82eXyK4my6MCW…> [A close-up of a logo Description automatically generated] Sign up to receive our monthly updates<https://secure-web.cisco.com/1EcNbd--t7q66h14Fxl_ENEIp5a1umwwa3y9OXMrD5_xUe…>

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errore with tracula: eddy_openmp: Command not found.
by Barletta, Valeria 03 Dec '24

03 Dec '24

Dear Freesurfers, I am trying to run trac-all on Freesurfer 7.4.1 but I am obtaining this output: eddy_openmp --imain=trac/R01121_SCAN/dmri/dwi_orig_las.nii.gz --mask=trac/R01121_SCAN/dmri/lowb_orig_las_brain_mask.nii.gz --bvecs=trac/R01121_SCAN/dmri/dwi_orig_las.bvecs --bvals=trac/R01121_SCAN/dmri/dwi_orig_las.bvals --acqp=trac/R01121_SCAN/dmri/acqp.txt --index=trac/R01121_SCAN/dmri/index.txt --data_is_shelled --out=trac/R01121_SCAN/dmri/dwi eddy_openmp: Command not found. Linux LAPTOP-OH2647G1 5.15.167.4-microsoft-standard-WSL2 #1 SMP Tue Nov 5 00:21:55 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Dec 3 20:11:28 CET 2024 Can you please help me understand the problem? Is that related to my FSL version? Thank you, Valeria

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trac-all -prep EDDY Unrealistic read-out time
by ADRIANA LUCIA RUIZ RIZZO 03 Dec '24

03 Dec '24

External Email - Use Caution Dear TRACULA experts, I'm trying to run TRACULA for one subject (multiple scans, longitudinal) but I'm getting the following error. Is there a way to fix this? I attach the b-vals and b-vecs. eddy_openmp --imain=/home/data/dsf4b/trc/sub-F4B002_2.long.sub-F4B002/dmri/dwi_orig_las.nii.gz --mask=/home/data/dsf4b/trc/sub-F4B002_2.long.sub-F4B002/dmri/lowb_topup_brain_mask.nii.gz --bvecs=/home/data/dsf4b/trc/sub-F4B002_2.long.sub-F4B002/dmri/dwi_orig_las.bvecs --bvals=/home/data/dsf4b/trc/sub-F4B002_2.long.sub-F4B002/dmri/dwi_orig_las.bvals --acqp=/home/data/dsf4b/trc/sub-F4B002_2.long.sub-F4B002/dmri/acqp.txt --index=/home/data/dsf4b/trc/sub-F4B002_2.long.sub-F4B002/dmri/index.txt --data_is_shelled --topup=/home/data/dsf4b/trc/sub-F4B002_2.long.sub-F4B002/dmri/topup --out=/home/data/dsf4b/trc/sub-F4B002_2.long.sub-F4B002/dmri/dwi EDDY::: AcqPara::AcqPara: Unrealistic read-out time EDDY::: EddyHelperClasses.cpp::: EDDY::AcqPara::AcqPara(const ColumnVector&, double): Exception thrown EDDY::: Eddy failed with message EDDY::: ECScanClasses.cpp::: EDDY::ECScanManager::ECScanManager(const string&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, EDDY::ECModel, EDDY::ECModel, const std::vector<unsigned int>&, const EDDY::PolationPara&, EDDY::MultiBandGroups, bool): Exception thrown The mentioned acquisition parameters are 0 -1 0 .000087629746 0 1 0 .000087629746 Thank you, Adriana -- _La información aquí contenida es para uso exclusivo de la persona o entidad de destino. Está estrictamente prohibida su utilización, copia, descarga, distribución, modificación y/o reproducción total o parcial, sin el permiso expreso de la Universidad de Antioquia, pues su contenido puede ser de carácter confidencial y/o contener material privilegiado. *La Universidad de Antioquia no se hace responsable por la información contenida en esta comunicación, el directo responsable es el egresado(a) que la firma como autor de la misma.* _ -- UdeA

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Take screenshot via sbatch without launching GUI
by Blujus, Jenna 02 Dec '24

02 Dec '24

External Email - Use Caution Hello, I have run vertex-wise cortical thickness analyses via command line (mris_preproc, mri_glmfit, mri_glmfit-sim) using Freesurfer v7.3.2 (freesurfer-linux-centos7_x86_64-7.3.2-20220804-6354275). I am now attempting to take a screenshot of the resulting significant clusters with Freeview. I am running multiple analyses so I set up an sbatch job to be submitted via our hpc cluster scheduler. The issue is that GUIs can't be launched via sbatch, so no screenshot is generated. I could do this via command line but I was hoping to automate the process. Is there any flag added or alternative approach that can be taken to generate the screenshot via sbatch jobs? Below is the command: freeview -f ${SUBJECTS_DIR}/fsaverage/surf/lh.inflated:overlay=lh.gender.glmdir/group.diff/cache.th30.abs.sig.cluster.mgh:overlay_threshold=1.3,5:annot=lh.gender.glmdir/group.diff/cache.th30.abs.sig.ocn.annot -viewport 3d -layout 1 -hide-3d-slices -hide-3d-frames -cam azimuth 180 -ss ${script_dir}/results_summary/results-${parent_folder}_${iv}_${crnt_combo}_med.jpg Error when run via sbatch: could not connect to display :1.0 This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem. Thanks, Jenna

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Fwd: recon-all command stuck before creating pial files
by chemda wiener 02 Dec '24

02 Dec '24

External Email - Use Caution Hi, My name is Chemda Wiener. I am a PhD student in a Neuro-Engineering lab. We are working with MRI scans of patients with epilepsy and I am attempting to use freesurfer to create the mesh .pial files. When I run the freesurfer recon-all command, the command gets stuck at "correcting defects" with the last file it creates being the "lh.defect_chull". It has been stuck for a few days on this part until I finally killed the process. I tried running autorecon2 afterwards on this patient to see if it can pick up from where it stopped but it gets stuck again at the same place. I would appreciate any help in the matter. Thank you in advance for your time and your software! Chemda

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unsubscrube
by Daria Sharapova 01 Dec '24

01 Dec '24

External Email - Use Caution Hi please unsubscribe me 81sharapova(a)gmail.com

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Merging aparc+aseg and ThalamicNuclei
by Andrew M 01 Dec '24

01 Dec '24

External Email - Use Caution I'm looking to merge the aparc+aseg.mgz with outputs from additional seg steps such as ThalamicNuclei (e.g., ThalamicNuclei.v13.T1T2.FSvoxelSpace.mgz) I see in history there used to be a function mergeseg, but maybe doesn't exist anymore? I also found in freesurfer/7.4.1/trctrain/hcp separate subject folders which have aparc+aseg+thalnuc.nii.gz, which is exactly what I'm looking for, except not in the correct space (hoping to keep in the same space as the original aparg+aseg, which ThalamicNuclei.v13.T1T2.FSvoxelSpace.mgz is in). Thank you! Andrew

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Pipeline for Transferring VBM Outputs to FreeSurfer and Parcellating with the Destrieux Atlas
by Safari, Nooshin (rvz7wf) 01 Dec '24

01 Dec '24

External Email - Use Caution Hi experts, I am working on transferring VBM output, which is in NIfTI format, to FreeSurfer space. I would like to follow this with parcellation using the Destrieux atlas, which is the standard with FreeSurfer. What is the pipeline to do this? Sincerely, Nooshin

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FDG Pet: How do I create an 'SUVR Image'?
by Lai, Ian M. 01 Dec '24

01 Dec '24

External Email - Use Caution I am quite inexperienced with the technology but have been asked to use PETSurfer to create a 'SUVR Image' of an FDG Pet scan, where the number associated with intensity in the motion-corrected, partial volume corrected value is the SUVR value. >From what I understand, an indication of success would be that the values on the mgx.gm.nii.gz being on the scale of around 1-10, rather than in the thousands. I have tried to achieve this by adding the --rescale 7 8 46 47 flag to the partial volume correction step, but the numbers are still in the order of the thousands. Is there any way to manually rescale the file's intensities, dividing the entire file's intensities by the average value across the cerebellum? Thank you for your help, please let me know if my question is unclear. Ian

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Recon-all failing
by Mark Wagshul 01 Dec '24

01 Dec '24

External Email - Use Caution Hi, I'm hoping someone can help with this strange error. Have been using recon-all on this dataset forever, and now all of a sudden it is completely failing just a few minutes into the processing. Attaching the recon-all.log file (had run a bunch of times, so only saved the last invocation in the file). It seems to get up to an mris_calc command to multiply the image by a scaling factor, but the number is missing. Here is the last bit of code where it fails: 7.2.0 cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.1410486/ones.mgz --i ./tmp.mri_nu_correct.mni.1410486/nu0.mgz --sum ./tmp.mri_nu_correct.mni.1410486/sum.junk --avgwf ./tmp.mri_nu_correct.mni.1410486/output.mean.dat sysname Linux hostname mwagshul machine x86_64 user mwagshul whitesurfname white UseRobust 0 Loading ./tmp.mri_nu_correct.mni.1410486/ones.mgz Loading ./tmp.mri_nu_correct.mni.1410486/nu0.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.1410486/output.mean.dat mri_segstats done Missing parameters. Usage: bc inputImageFile inputSegmentationFile side PathToTrainingFiles outputSegmentationFile side = 0 (left side) or else (right side) mris_calc -o ./tmp.mri_nu_correct.mni.1410486/nu0.mgz ./tmp.mri_nu_correct.mni.1410486/nu0.mgz mul Segmentation fault (core dumped) Thanks so much in advance for any advice! Best, Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einsteinmed.edu<mailto:mark.wagshul@einsteinmed.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

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Freesurfer December 2024