Freesurfer

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Tracula prepocessing error awk: fatal: cannot open file dmri/dwi_orig_las.1.bvals
by Vicente Ferrer 07 Feb '22

07 Feb '22

External Email - Use Caution Hi all, I was trying to run trac-all preprocessing and it seems there is a problem with eddy_openmp. The program is unable to find the dwi_orig_las.1.bvals file which makes that the index.txt is empty. see the terminal output: trac-all -prep -c tracula_config INFO: SUBJECTS_DIR is /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI INFO: Diffusion root is /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI Actual FREESURFER_HOME /share/opt/freesurfer-7.2.0 INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b trac-preproc -c /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/scripts/dmrirc.local -log /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/scripts/trac-all.log -cmd /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/scripts/trac-all.cmd #------------------------------------- /opt/freesurfer-7.2.0/bin/trac-preproc #------------------------------------- #@# Image corrections Mon Feb 7 15:56:50 CET 2022 rm -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvals /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvecs mri_convert --bvec-voxel /bcbl/home/public/PD_ANALYSIS/BIDS_DWI/sub-3102/ses-Session_baseline/dwi/sub-3102_ses-Session_baseline_run-_dwi.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz mri_convert --bvec-voxel /bcbl/home/public/PD_ANALYSIS/BIDS_DWI/sub-3102/ses-Session_baseline/dwi/sub-3102_ses-Session_baseline_run-_dwi.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz reading from /bcbl/home/public/PD_ANALYSIS/BIDS_DWI/sub-3102/ses-Session_baseline/dwi/sub-3102_ses-Session_baseline_run-_dwi.nii.gz... TR=900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1e-16, 0) j_ras = (1e-16, 0.92521, 0.379456) k_ras = (-3.79456e-17, -0.379456, 0.92521) writing to /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz... rm -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvals.tmp /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvecs.tmp mv -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvecs.tmp /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvecs mv -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvals.tmp /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvals orientLAS /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -7.86266 mri_convert -oni 116 -onj 116 -onk 72 -oid -1 1e-16 0 -ojd 1e-16 0.92521 0.379456 -okd -3.79456e-17 -0.379456 0.92521 -oc 2.02404 20.3466 -11.1417 -rt nearest /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.nii.gz mri_convert -oni 116 -onj 116 -onk 72 -oid -1 1e-16 0 -ojd 1e-16 0.92521 0.379456 -okd -3.79456e-17 -0.379456 0.92521 -oc 2.02404 20.3466 -11.1417 -rt nearest /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.nii.gz normalizing out_j_direction: (1e-16, 0.92521, 0.379456) -> (1e-16, 0.92521, 0.379456) normalizing out_k_direction: (-3.79456e-17, -0.379456, 0.92521) -> (-3.79456e-17, -0.379456, 0.92521) reading from /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.nii.gz... TR=900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1e-16, 0) j_ras = (1e-16, 0.92521, 0.379456) k_ras = (-3.79456e-17, -0.379456, 0.92521) Reslicing using nearest writing to /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.nii.gz... INFO: found /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvals, copying INFO: found /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig.1.bvecs, converting to LAS mv -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.nii.gz mv -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.bvecs /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.bvecs mv -f /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.bvals /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.bvals mri_convert --frame 0 /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/lowb_orig_las.nii.gz mri_convert --frame 0 /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/lowb_orig_las.nii.gz reading from /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.nii.gz... TR=900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 1e-16, 0) j_ras = (1e-16, 0.92521, 0.379456) k_ras = (-3.79456e-17, -0.379456, 0.92521) keeping frame 0 writing to /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/lowb_orig_las.nii.gz... bet /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/lowb_orig_las.nii.gz /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/lowb_orig_las_brain.nii.gz -m -f 0.3 awk: fatal: cannot open file `/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.1.bvals' for reading (No such file or directory) eddy_openmp --imain=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.nii.gz --mask=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/lowb_orig_las_brain_mask.nii.gz --bvecs=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.bvecs --bvals=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi_orig_las.bvals --acqp=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/acqp.txt --index=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/index.txt --data_is_shelled --out=/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/sub-3102ses-Session_baseline_final/dmri/dwi EddyInputError: Error when attempting to read --index file Terminating program Linux ipsnode-7-2.local 3.10.0-693.21.1.el7.x86_64 #1 SMP Wed Mar 7 19:03:37 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Mon Feb 7 15:57:40 CET 2022 I checked the dmri directory and there is no dwi_orig_las.1.bvals. However there is a file named `dwi_orig_las.bvals`. Could the issue be that the file is not properly named? Thanks in advance Vicente Ferrer Predoctoral Researcher BCBL http://secure-web.cisco.com/1-Ku-hldgDaWjT-BvD-_pMWqml40Goi5g72COU-9PXhhnvl… Legal disclaimer/Aviso legal/Lege-oharra: http://secure-web.cisco.com/1nEcXGCtYms2UHA-p-uSmLLk_ufUH4B0eX4xXxtgSq9z_K3…

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Re: [Freesurfer] virtual machine password
by fsbuild 07 Feb '22

07 Feb '22

External Email - Use Caution Sending to your email shortly. - R. On Feb 6, 2022, at 01:30, sina hospital <sina6312(a)gmail.com> wrote:        External Email - Use Caution        Greetings and RegardsPlease give me the ubuntu virtual machine passwordThanks_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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virtual machine password
by sina hospital 06 Feb '22

06 Feb '22

External Email - Use Caution Greetings and Regards Please give me the ubuntu virtual machine password Thanks

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Re: [Freesurfer] Developer login
by fsbuild 05 Feb '22

05 Feb '22

External Email - Use Caution Sending the info to your email shortly. - R. On Feb 5, 2022, at 14:59, Guillaume Pech <mfb.pech(a)gmail.com> wrote:        External Email - Use Caution        Hello, I am installing Free-Surver via the VirtualBox and I need the password for the developer account please. Thanks _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Developer login
by Guillaume Pech 05 Feb '22

05 Feb '22

1 0

developer login
by Guillaume Pech 05 Feb '22

05 Feb '22

1 0

Developer Login
by Guillaume Pech 05 Feb '22

05 Feb '22

1 0

Re: [Freesurfer] Updated Mac to Monterey, issues with Freesurfer
by fsbuild 04 Feb '22

04 Feb '22

External Email - Use Caution Hello Lisa, Are you running the 7.2.0 release, e.g. as installed by the package installer,  https://secure-web.cisco.com/1WrA-NZx66e293R6KJNdyTGSNLLRCP3adzgCpi5RDIvdwv… ?? After the package install, it will be listed in the Finder as /Applications/freesurfer/7.2.0 - R. On Feb 4, 2022, at 17:15, Taylor, Lisa <ltaylor2(a)hs.uci.edu> wrote:        External Email - Use Caution        Hi there, Not exactly sure if you'll be able to help but I am a bit stumped. I recently updated my MAC os to the new monterey update. I now get these error messages when trying to use Freesurfer, or even freeview:viewfreesurfer PATH/MRI/Freesurfer 2022-02-04 09:50:46.970 Freeview[476:2201959] *** WARNING: Method userSpaceScaleFactor in class NSView is deprecated on 10.7 and later. It should not be used in new applications. Use convertRectToBacking: instead. [unset]: aborting job:application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0viewfreesurfer:4: command not found: [0]PETSC[\w]$ freeview2022-02-04 09:51:20.263 Freeview[777:2204165] *** WARNING: Method userSpaceScaleFactor in class NSView is deprecated on 10.7 and later. It should not be used in new applications. Use convertRectToBacking: instead. [0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger[0]PETSC ERROR: or see http://secure-web.cisco.com/1ms4uWzVnFfUyjwx3Q4TOmbOyaHG14QccfYH-M…: or try http://secure-web.cisco.com/1NcuTEBWMPSP0hSarumWN6v5_tx3tAZjQ4BCPG… linux or man libgmalloc on Apple to find memory corruption errors[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash.[0]PETSC ERROR: --------------------- Error Message ------------------------------------[0]PETSC ERROR: Signal received![0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124[0]PETSC ERROR: See docs/changes/index.html for recent updates.[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.[0]PETSC ERROR: See docs/index.html for manual pages.[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: Unknown Name on a darwin12. named Taylor-Desktop.local by taylorl Fri Feb  4 09:51:18 2022[0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt[0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012[0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3[0]PETSC ERROR: ------------------------------------------------------------------------[0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file[unset]: aborting job:application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0I am not exactly tech savvy to understand how I can go about this to remedy it. Any advice?Thank you so much..LisaThis message may contain confidential information and is for the sole use of the intended recipient(s). If you are not the intended recipient, do not use, distribute, or copy this e-mail. Please notify the UC Irvine Health – Compliance and Privacy Office via email at hacompliance(a)uci.edu or by phone 888-456-7006 immediately if you have received this e-mail in error. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Updated Mac to Monterey, issues with Freesurfer
by Taylor, Lisa 04 Feb '22

04 Feb '22

External Email - Use Caution Hi there, Not exactly sure if you'll be able to help but I am a bit stumped. I recently updated my MAC os to the new monterey update. I now get these error messages when trying to use Freesurfer, or even freeview: viewfreesurfer PATH/MRI/Freesurfer 2022-02-04 09:50:46.970 Freeview[476:2201959] *** WARNING: Method userSpaceScaleFactor in class NSView is deprecated on 10.7 and later. It should not be used in new applications. Use convertRectToBacking: instead. [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 viewfreesurfer:4: command not found: [0]PETSC [\w]$ freeview 2022-02-04 09:51:20.263 Freeview[777:2204165] *** WARNING: Method userSpaceScaleFactor in class NSView is deprecated on 10.7 and later. It should not be used in new applications. Use convertRectToBacking: instead. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://secure-web.cisco.com/1EG_EG7NKVy2YlczWKlaltWyiZxVvICvRft1yFkkckKjOYb… ERROR: or try http://secure-web.cisco.com/1GqQtB0MZCxTV0bZHhEXv3QNy3VG7-5YvXgfSDW1Lq0ByRH… on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a darwin12. named Taylor-Desktop.local by taylorl Fri Feb 4 09:51:18 2022 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 I am not exactly tech savvy to understand how I can go about this to remedy it. Any advice? Thank you so much. Lisa ________________________________ This message may contain confidential information and is for the sole use of the intended recipient(s). If you are not the intended recipient, do not use, distribute, or copy this e-mail. Please notify the UC Irvine Health – Compliance and Privacy Office via email at hacompliance(a)uci.edu or by phone 888-456-7006 immediately if you have received this e-mail in error. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

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Question glm analysis
by Laura Willers de Souza 04 Feb '22

04 Feb '22

External Email - Use Caution Hello FreeSurfer Developers, I am performing a GLM analysis to assess cortical thickness between 4 groups, without any covariates. I followed exactly what is on the wiki https://secure-web.cisco.com/1OE5gTnSPStX6C1rqwHBKIDpqIcnp_2ymvTKb8n7oDB8Ix… In a previous analysis (https://secure-web.cisco.com/1I4SmLAoporSfSSXp8cqB6-whkM3uuzSOJ6T9fT_OfoVtM…) Dr Douglas had told me that before any analysis I should test whether the interaction is significant or not. I would like to know if this also applies to this case, the interaction being tested by contrast number 7 of the wiki. Thanks in advance! Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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