Yes you probably need to have bash instead of a non-bash shell. Perhaps fixing that will solve the problem. As far as the resolution of the T1w and T2w, presumably so long as they are the same resolution everything should work. We have tested on 0.8mm human data and 0.5mm monkey data.
Matt. From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Date: Friday, November 9, 2018 at 3:53 PM To: "Jayasekera, Dinal" <dinal.jayasek...@wustl.edu<mailto:dinal.jayasek...@wustl.edu>>, Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "Dierker, Donna" <do...@wustl.edu<mailto:do...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Debugging IcaFIxProcessingBatch.sh 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<mailto: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<mailto:tsc...@mst.edu>> Sent: Thursday, November 8, 2018 6:03:10 PM To: Jayasekera, Dinal Cc: Dierker, Donna; hcp-users@humanconnectome.org<mailto: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<mailto: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/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<mailto: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<mailto: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<mailto: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<mailto: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<mailto:dinal.jayasek...@wustl.edu>> > Date: Thursday, November 1, 2018 at 8:32 PM > To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "Harms, > Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, > "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" > <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> > Cc: Timothy Coalson <tsc...@mst.edu<mailto: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<mailto: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<mailto:hcp-users-boun...@humanconnectome.org>> > on behalf of "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> > Date: Thursday, November 1, 2018 at 4:18 PM > To: "Jayasekera, Dinal" > <dinal.jayasek...@wustl.edu<mailto:dinal.jayasek...@wustl.edu>>, > "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" > <hcp-users@humanconnectome.org<mailto: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<http://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<mailto:mha...@wustl.edu> > > From: > <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> > on behalf of "Jayasekera, Dinal" > <dinal.jayasek...@wustl.edu<mailto:dinal.jayasek...@wustl.edu>> > Date: Thursday, November 1, 2018 at 4:10 PM > To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" > <hcp-users@humanconnectome.org<mailto: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<mailto: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<mailto:HCP-Users@humanconnectome.org> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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
