I forgot to attach the matlab dump file.
Kind regards, Dinal Jayasekera PhD Candidate | InSITE Fellow Ammar Hawasli Lab Department of Biomedical Engineering | Washington University in St. Louis ________________________________ From: Jayasekera, Dinal Sent: Thursday, November 8, 2018 1:36:15 PM To: Dierker, Donna Cc: Glasser, Matthew; Harms, Michael; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh Dear Donna, I apologize for the late reply. I've been trying different approaches to solve the errors I've been receiving. I've attached the updated log files after re-configuring the R packages. This was the output to stdout and stderr: rfMRI_REST1_PA_hp2000.ica/mc: total 32 drwxrwxr-x 2 functionalspinelab functionalspinelab 4096 Oct 31 19:12 . drwxrwxr-x 6 functionalspinelab functionalspinelab 4096 Nov 7 15:57 .. -rw-rw-r-- 1 functionalspinelab functionalspinelab 20936 Nov 7 15:57 prefiltered_func_data_mcf.par rfMRI_REST1_PA_hp2000.ica/reg: total 41680 drwxrwxr-x 2 functionalspinelab functionalspinelab 4096 Nov 7 15:57 . drwxrwxr-x 6 functionalspinelab functionalspinelab 4096 Nov 7 15:57 .. lrwxrwxrwx 1 functionalspinelab functionalspinelab 19 Nov 7 15:57 example_func.nii.gz -> ../mean_func.nii.gz lrwxrwxrwx 1 functionalspinelab functionalspinelab 36 Nov 7 15:57 highres.nii.gz -> ../../../../T1w_restore_brain.nii.gz -rw-rw-r-- 1 functionalspinelab functionalspinelab 149 Nov 7 15:57 highres2example_func.mat -rw-rw-r-- 1 functionalspinelab functionalspinelab 42190921 Nov 7 15:57 veins.nii.gz -rw-rw-r-- 1 functionalspinelab functionalspinelab 473780 Nov 7 15:57 veins_exf.nii.gz lrwxrwxrwx 1 functionalspinelab functionalspinelab 25 Nov 7 15:57 wmparc.nii.gz -> ../../../../wmparc.nii.gz hcp_fix: INFORM: functionmotionconfounds log file is to be named: .fix.functionmotionconfounds.log instead of .fix.log hcp_fix: DEBUG: current folder /home/functionalspinelab/Desktop/Dinal/mystudy/NSI_12/MNINonLinear/Results/rfMRI_REST1_PA/rfMRI_REST1_PA_hp2000.ica/reg Mask and image must be the same size Image Exception : #63 :: No image files match: -mul Image Exception : #22 :: Failed to read volume -mul Error : No image files match: -mul terminate called after throwing an instance of 'armawrap::AWException' what(): Failed to read volume -mul Error : No image files match: -mul Aborted (core dumped) hcp_fix: INFORM: running FIX /home/functionalspinelab/Desktop/Dinal/Pipelines/ICAFIX/hcp_fix: 171: /home/functionalspinelab/Desktop/Dinal/Pipelines/ICAFIX/hcp_fix: [[: not found hcp_fix: INFORM: About to run: /home/functionalspinelab/Desktop/Dinal/Applications/fix1.066/fix rfMRI_REST1_PA_hp2000.ica /home/functionalspinelab/Desktop/Dinal/Applications/fix1.066/training_files/HCP_hp2000.RData 10 -m -h 2000 FIX Feature extraction for Melodic output directory: rfMRI_REST1_PA_hp2000.ica create edge masks run FAST registration of standard space masks flirt: symbol lookup error: flirt: undefined symbol: dgesdd_ extract features FIX Classifying components in Melodic directory: rfMRI_REST1_PA_hp2000.ica using training file: /home/functionalspinelab/Desktop/Dinal/Applications/fix1.066/training_files/HCP_hp2000.RData and threshold 10 No valid labelling file specified Could not find a supported file with prefix "rfMRI_REST1_PA_hp2000.ica/filtered_func_data_clean" Could not find a supported file with prefix "rfMRI_REST1_PA_hp2000.ica/filtered_func_data_clean_vn" I'm receiving a segmentation error which is causing MATLAB to exit. Any thoughts? Kind regards, Dinal Jayasekera PhD Candidate | InSITE Fellow Ammar Hawasli Lab Department of Biomedical Engineering | Washington University in St. Louis ________________________________ From: Dierker, Donna Sent: Saturday, November 3, 2018 7:39:51 AM To: Jayasekera, Dinal Cc: Glasser, Matthew; Harms, Michael; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh Check not only your standard output file, but also your standard error. Do either indicate whether it is finding matlab/octave? > On Nov 2, 2018, at 3:02 PM, Jayasekera, Dinal <dinal.jayasek...@wustl.edu> > wrote: > > Dear Michael and Matt, > > I reconfigured R, updated sICA+FIX and FSL but I still continue to get the > previous error: > > No valid labelling file specified > Could not find a supported file with prefix > "rfMRI_REST1_AP_hp2000.ica/filtered_func_data_clean" > Could not find a supported file with prefix > "rfMRI_REST1_AP_hp2000.ica/filtered_func_data_clean_vn" > > > Do you have any other suggestions? > > > Kind regards, > Dinal Jayasekera > > PhD Candidate | InSITE Fellow > Ammar Hawasli Lab > Department of Biomedical Engineering | Washington University in St. Louis > > From: Jayasekera, Dinal > Sent: Thursday, November 1, 2018 8:35:28 PM > To: Glasser, Matthew; Harms, Michael; hcp-users@humanconnectome.org > Cc: NEUROSCIENCE tim > Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh > > Oh yes definitely not. I also upgraded my R packages. > > > Kind regards, > Dinal Jayasekera > > PhD Candidate | InSITE Fellow > Ammar Hawasli Lab > Department of Biomedical Engineering | Washington University in St. Louis > > From: Glasser, Matthew > Sent: Thursday, November 1, 2018 8:33:58 PM > To: Jayasekera, Dinal; Harms, Michael; hcp-users@humanconnectome.org > Cc: NEUROSCIENCE tim > Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh > > That doesn’t discount Mike’s advice on needing to sort out R packages. > > Matt. > > From: "Jayasekera, Dinal" <dinal.jayasek...@wustl.edu> > Date: Thursday, November 1, 2018 at 8:32 PM > To: Matt Glasser <glass...@wustl.edu>, "Harms, Michael" <mha...@wustl.edu>, > "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Cc: Timothy Coalson <tsc...@mst.edu> > Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh > > Matt, > > I will update my version of sICA+FIX as well and upgrade to FSL 6.0 and let > you know how things change. > > > Kind regards, > Dinal Jayasekera > > PhD Candidate | InSITE Fellow > Ammar Hawasli Lab > Department of Biomedical Engineering | Washington University in St. Louis > > From: Glasser, Matthew > Sent: Thursday, November 1, 2018 6:56:26 PM > To: Harms, Michael; Jayasekera, Dinal; hcp-users@humanconnectome.org > Cc: NEUROSCIENCE tim > Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh > > Hi Dinal, > > Also make sure you have the absolutely latest version of sICA+FIX, as there > were recent changes and upgrade to FSL 6.0. Finally, we are testing some > updates to hcp_multi_run_fix that you will need to be using for your project, > and we can let you know when that is available. For your project you will be > cleaning all of the fMRI runs at the same time with multi-run fix. > > Matt. > > From: <hcp-users-boun...@humanconnectome.org> on behalf of "Harms, Michael" > <mha...@wustl.edu> > Date: Thursday, November 1, 2018 at 4:18 PM > To: "Jayasekera, Dinal" <dinal.jayasek...@wustl.edu>, > "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh > > > Hi, > Have you configured your R installation correctly, per the FSL FIX Wiki page? > > https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/UserGuide FIX/UserGuide - FslWiki - University of Oxford<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/UserGuide> fsl.fmrib.ox.ac.uk Downloading and Installing FIX. Requirements: FSL. MATLAB (though see notes in Introduction page), with official toolboxes: Statistics ; Signal Processing > > cheers, > -MH > > -- > Michael Harms, Ph.D. > ----------------------------------------------------------- > Associate Professor of Psychiatry > Washington University School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: <hcp-users-boun...@humanconnectome.org> on behalf of "Jayasekera, > Dinal" <dinal.jayasek...@wustl.edu> > Date: Thursday, November 1, 2018 at 4:10 PM > To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org> > Subject: [HCP-Users] Debugging IcaFIxProcessingBatch.sh > > Dear HCP community, > > I am currently running the IcaFixProcessingBatch script on the data > processing using the minimal functional pipelines. However, for each of my > resting state conditions, I get the following error: > > /home/Desktop/Applications/fix1.066/fix: 252: > /home/Desktop/Applications/fix1.066/fix: R: not found > No valid labelling file specified > Could not find a supported file with prefix > "rfMRI_REST1_AP_hp2000.ica/filtered_func_data_clean" > > Has anyone had any experience with a similar issue? Is this error indicative > of a missing step from before? > > Kind regards, > Dinal Jayasekera > > PhD Candidate | InSITE Fellow > Ammar Hawasli Lab > Department of Biomedical Engineering | Washington University in St. Louis > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you are > not the intended recipient, be advised that any unauthorized use, disclosure, > copying or the taking of any action in reliance on the contents of this > information is strictly prohibited. If you have received this email in error, > please immediately notify the sender via telephone or return mail. > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
matlab_crash_dump.58103-1
Description: matlab_crash_dump.58103-1
