Here is the line from hcp_fix where it uses a 0.7mm mask:
$FSLDIR/bin/fslmaths veins -div `$FSLDIR/bin/fslstats veins -k
${FSL_FIXDIR}/mask_files/hcp_0.7mm_brain_mask -P 50` -mul 2.18 -thr 10 -min
50 -div 50 veins
https://github.com/Washington-University/HCPpipelines/blob/master/ICAFIX/hcp_fix#L159
So, the script hardcodes a path to a 0.7mm mask.
Tim
On Fri, Nov 9, 2018 at 7:13 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
> 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>
> Date: Friday, November 9, 2018 at 3:53 PM
> To: "Jayasekera, Dinal" <dinal.jayasek...@wustl.edu>, Matt Glasser <
> glass...@wustl.edu>
> Cc: "Dierker, Donna" <do...@wustl.edu>, "hcp-users@humanconnectome.org" <
> 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> 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/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/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.
>> > _______________________________________________
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>>
>
> ------------------------------
>
> 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.
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