This is the first problem I see in the text you pasted in the email: Mask and image must be the same size
This looks like it will happen whenever your T1w and T2w are not 0.7mm, as it specifically uses a 0.7mm mask. Someone else (Matt?) will need to say how this is supposed to work. Unfortunately, what I recommended was only for solving this error (and related): flirt: symbol lookup error: flirt: undefined symbol: dgesdd_ I was hoping that the earlier errors were caused by a similar undefined symbol error that you hadn't seen. As for this one, for some reason hcp_fix asked for the ancient behavior of /bin/sh at the top of the file, rather than /bin/bash: /home/functionalspinelab/Desktop/Dinal/Pipelines/ICAFIX/hcp_fix: 171: /home/functionalspinelab/Desktop/Dinal/Pipelines/ICAFIX/hcp_fix: [[: not found Tim On Fri, Nov 9, 2018 at 3:07 PM, Jayasekera, Dinal < dinal.jayasek...@wustl.edu> wrote: > Dear Tim, > > > I made the changes you recommended but I continue to receive the same > segmentation error I mentioned before. > > > Kind regards, > *Dinal Jayasekera* > > PhD Candidate | InSITE Fellow > Ammar Hawasli Lab > Department of Biomedical Engineering | Washington University in St. Louis > > ------------------------------ > *From:* Timothy Coalson <tsc...@mst.edu> > *Sent:* Thursday, November 8, 2018 6:03:10 PM > *To:* Jayasekera, Dinal > *Cc:* Dierker, Donna; hcp-users@humanconnectome.org > > *Subject:* Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh > > FSL 6 requires openblas, and specifically a build of openblas that > contains lapack symbols, which is not the case for the system-supplied on > in ubuntu 14.04. Via instructions on https://www.openblas.net/, clone > the source from github, build manually, and install to /usr/local (it is > important to install it there because of how we deal with matlab changing > library paths - if you don't want to install it there, you will need to > resort to wrapper scripts around fsl binaries, or other trickery), and run > "ldconfig" so that it will be found by default, like this (minorly edited > from a container recipe I am working with): > > sudo apt-get install build-essential > git clone https://github.com/xianyi/OpenBLAS.git --branch release-0.3.0 > --depth 5 > cd OpenBLAS > #you could specify a TARGET to optimize for your cpu here > make > sudo make PREFIX=/usr/local install > sudo ldconfig > > Tim > > > On Thu, Nov 8, 2018 at 1:36 PM, Jayasekera, Dinal < > dinal.jayasek...@wustl.edu> wrote: > > 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/Deskt > op/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/Deskt > op/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/Deskt > op/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/fil > tered_func_data_clean" > Could not find a supported file with prefix "rfMRI_REST1_PA_hp2000.ica/fil > tered_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 > <https://maps.google.com/?q=8134+%0D%0A+660+South+Euclid+Ave&entry=gmail&source=g> > > 660 South Euclid Ave > <https://maps.google.com/?q=8134+%0D%0A+660+South+Euclid+Ave&entry=gmail&source=g>. > 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 > > > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
