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Re: [Freesurfer] TRACULA exited with ERROR /home/vbarletta/ants-2.5.4/bin/antsRegistrationSyNQuick.sh: Permission denied.
by fsbuild 04 Dec '24

04 Dec '24

External Email - Use Caution Not sure how you setup/installed ants in your home directory, but it could be the install permissions are wrong on antsRegistrationSyNQuick.sh.  You could try making that script executable with, $ chmod 755 /home/vbarletta/ants-2.5.4/bin/antsRegistrationSyNQuick.sh - R. On Dec 4, 2024, at 16:48, Barletta, Valeria <VBARLETTA(a)mgh.harvard.edu> wrote:Dear Freesurfers,Do you know how to fix this error in trac-all? (I'm using Ubuntu 18.04) #@# Inter-subject registration Wed Dec  4 22:37:52 CET 2024/home/vbarletta/ants-2.5.4/bin/antsRegistrationSyNQuick.sh -d 3 -m trac/R01121_SCAN/dmri/dtifit_FA.nii.gz -f /home/vbarletta/tester/freesurfer/trctrain/hcp/MGH35_HCP_FA_template.nii.gz -o trac/R01121_SCAN/dmri/xfms/diff2syn/home/vbarletta/ants-2.5.4/bin/antsRegistrationSyNQuick.sh: Permission denied. trac-preproc exited with ERRORS at Wed Dec  4 22:37:52 CET 2024 Alternatively, is there a way to run Tracula without using ants? Thank you for your help,Valeria _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail..nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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TRACULA exited with ERROR /home/vbarletta/ants-2.5.4/bin/antsRegistrationSyNQuick.sh: Permission denied.
by Barletta, Valeria 04 Dec '24

04 Dec '24

Dear Freesurfers, Do you know how to fix this error in trac-all? (I'm using Ubuntu 18.04) #@# Inter-subject registration Wed Dec 4 22:37:52 CET 2024 /home/vbarletta/ants-2.5.4/bin/antsRegistrationSyNQuick.sh -d 3 -m trac/R01121_SCAN/dmri/dtifit_FA.nii.gz -f /home/vbarletta/tester/freesurfer/trctrain/hcp/MGH35_HCP_FA_template.nii.gz -o trac/R01121_SCAN/dmri/xfms/diff2syn /home/vbarletta/ants-2.5.4/bin/antsRegistrationSyNQuick.sh: Permission denied. trac-preproc exited with ERRORS at Wed Dec 4 22:37:52 CET 2024 Alternatively, is there a way to run Tracula without using ants? Thank you for your help, Valeria

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use and registration of FLAIR in recon-all and segmentHA
by Simone Cauzzo 04 Dec '24

04 Dec '24

External Email - Use Caution Hi all I am running Freesurfer 7.4 I use recon-all with the -FLAIRpial option. 1) I wonder whether the FLAIR to T1 registration is handled by recon-all or whether I need to supply a FLAIR image already registered to T1. 2) in case recon-all handles the registration, is there a way I can check the registration quality? which file should I use in freeview? 3) in case I already have a reliable FLAIR to T1 registration, is there a way to make recon-all skip the FLAIR to T1 registration? In addition, I would like to use segmentHA_T2.sh 4) in case recon-all handles the registration, which file can I give to segmentHA_T2 as additional scan? I guess I should select the FLAIR already registered to T1.. 5) Is there a reason why I should prefer a T2 image to a FLAIR for segmentHA_T2? Thank you Simone Cauzzo, PhD University of Padova

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Re: [Freesurfer] mri_coreg threads parallel processing clarification
by fsbuild 04 Dec '24

04 Dec '24

External Email - Use Caution You could try setting the environment variable OMP_NUM_THREADS, e.g., in zsh/bash shell,  on a machine with 4 performance cores, $ export OMP_NUM_THREADS=4 The test command I ran did not take long to run, but it looks like it used 3 of the 4 performance cores on an M1 Mac with OMP_NUM_THREADS=4.  See attached screenshot, mri_coreg_omp_num_threads.png - R. On Dec 3, 2024, at 17:06, Hemond, Christopher <Christopher.Hemond(a)umassmemorial.org> wrote:        External Email - Use Caution        Dear Doug and team,Thanks very much for your support.  I’ve tried multiple different thread numbers between 1 and 10 with no effect.  I can successfully use multithreading to accelerate other applications like mri_synthseg.I tried adding combinations of both ‘fs_time’ as well as ‘--debug’  to the command, but I do not see any difference in final output, nor any CPU load/usage readout at the end of the command….  Just the usual “mri_coreg RunTimeSec <X> sec”.  Could this be related to the ARM processor in Mac?  It seems to cause many other issues, especially with some SPM commands including processing specification.Many thanks,Chris  From: Hemond, Christopher <Christopher.Hemond(a)umassmemorial.org> Date: Monday, November 25, 2024 at 4:32 PM To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> Subject: mri_coreg threads parallel processing clarificationDear experts,Thanks in advance for any help you can provide.  I’m using “mri_coreg” and trying to accelerate it with the “--threads” (and/or “--nthreads”) flags. However in the subsequent command feedback it looks like it is still using just one thread (see output below, “nthreads 1”; and also it is no faster).  Am I doing something obviously wrong?  There are no errors and it executes successfully…   Not sure if relevant but I’m using this for nifty (.nii.gz) files, my command is:“mri_coreg --ref <path/to/ref.nii.gz> --mov <path/to/mov.nii.gz> --reg <path/to/registration.lta> --threads 10” I’m on MacOS running a recent dev download (freesurfer-macOS-darwin_arm64-dev-20241011), but I’ve tried it on 7..4.1 with no success either.  …INFO: using NIfTI-1 sform (sform_code=1)Setting cras translation parameters to align volume centersInit matrix params -0.4553 -6.3123 39.4428  0.0000  0.0000  0.0000  1.0000  1.0000  1.0000  0.0000  0.0000  0.0000 Initial Matrix (RAS2RAS) 1.00000   0.00000   0.00000   0.45535; 0.00000   1.00000   0.00000   6..31235; 0.00000   0.00000   1.00000  -39.44280; 0.00000   0.00000   0.00000   1.00000;Initial parameters to be opt -0.4553 -6.3123 39.4428  0.0000  0.0000  0.0000 Creating random numbers for coordinate ditheringPerforming intensity ditheringPerforming intensity dithering on mov with computed ditherSeparation list (2):  4  2   min = 2DoSmoothing 1DoCoordDither 1DoIntensityDither 1nitersmax 4ftol 1.000e-07linmintol 1.000e-03SatPct 99.990000Hist FWHM 7.000000 7.000000nthreads 1movsat = 3917.0000mov gstd 0.9539 0.9539 0..7422Smoothing mov… The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, transmission, re-transmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_coreg threads parallel processing clarification
by Hemond, Christopher 03 Dec '24

03 Dec '24

External Email - Use Caution Dear experts, Thanks in advance for any help you can provide. I’m using “mri_coreg” and trying to accelerate it with the “--threads” (and/or “--nthreads”) flags. However in the subsequent command feedback it looks like it is still using just one thread (see output below, “nthreads 1”; and also it is no faster). Am I doing something obviously wrong? There are no errors and it executes successfully… Not sure if relevant but I’m using this for nifty (.nii.gz) files, my command is: “mri_coreg --ref <path/to/ref.nii.gz> --mov <path/to/mov.nii.gz> --reg <path/to/registration.lta> --threads 10” I’m on MacOS running a recent dev download (freesurfer-macOS-darwin_arm64-dev-20241011), but I’ve tried it on 7.4.1 with no success either. … INFO: using NIfTI-1 sform (sform_code=1) Setting cras translation parameters to align volume centers Init matrix params -0.4553 -6.3123 39.4428 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Initial Matrix (RAS2RAS) 1.00000 0.00000 0.00000 0.45535; 0.00000 1.00000 0.00000 6.31235; 0.00000 0.00000 1.00000 -39.44280; 0.00000 0.00000 0.00000 1.00000; Initial parameters to be opt -0.4553 -6.3123 39.4428 0.0000 0.0000 0.0000 Creating random numbers for coordinate dithering Performing intensity dithering Performing intensity dithering on mov with computed dither Separation list (2): 4 2 min = 2 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-07 linmintol 1.000e-03 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 3917.0000 mov gstd 0.9539 0.9539 0.7422 Smoothing mov … The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, transmission, re-transmission, dissemination or other use of, or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error, please contact the sender and delete the material from any computer.

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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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