ICA Fix processing
Mary Huynh
I am currently following the HCP pipeline to process ASL data. I am new to the pipeline so any guidance is appreciated. I processed only the ASL data (just looking at 1 fMRI task, i.e. mbpcaslhr_PA) using the volume and surface processing pipelines. Now, I am currently on the IcaFixProcessingBatch.sh step but have run into errors (see below). I will also attach my ICA script as well in case I have put in the wrong inputs. Thank you in advance!
tail hcp_fix.o12995
FIX Feature extraction for Melodic output directory: mbpcaslhr_PA_hp2000.ica
create edge masks
run FAST
registration of standard space masks
extract features
No valid labelling file specified
Mon Feb 3 13:07:01 EST 2025:hcp_fix: Done running FIX
Could not find a supported file with prefix "mbpcaslhr_PA_hp2000.ica/filtered_func_data_clean"
Mon Feb 3 13:07:02 EST 2025:hcp_fix: While running '/mnt/c/Users/maryk/MRI/HCPpipelines-5.0.0/ICAFIX/hcp_fix /mnt/c/Users/maryk/MRI/hcp_asl/00101/MNINonLinear/Results/mbpcaslhr_PA/mbpcaslhr_PA 2000 FALSE HCP_hp2000.RData 10 FALSE':
Mon Feb 3 13:07:02 EST 2025:hcp_fix: ERROR: '/usr/local/fsl/bin/immv' command failed with return code: 1
more hcp_fix.e12995
Mon Feb 10 13:07:02 EST 2025:hcp_fix: While running '/mnt/c/Users/maryk/MRI/HCPpipelines-5.0.0/ICAFIX/hcp_fix /mnt/c/Use
rs/maryk/MRI/hcp_asl/00101/MNINonLinear/Results/mbpcaslhr_PA/mbpcaslhr_PA 2000 FALSE HCP_hp2000.RData 10 FALSE':
Mon Feb 10 13:07:02 EST 2025:hcp_fix: ERROR: '/usr/local/fsl/bin/immv' command failed with return code: 1
===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
script: hcp_fix
stopped at line: 462
call: $FSLDIR/bin/immv ${fmrihp}.ica/filtered_func_data_clean ${fmrihp}_clean
expanded call: /usr/local/fsl/bin/immv mbpcaslhr_PA_hp2000.ica/filtered_func_data_clean mbpcaslhr_PA_hp2000_clean
hostname: DESKTOP-IOLFI62
exit code: 1
---------------------------------------------------
===> Aborting execution!
* MATLAB command window output *
Warning: Unrecognized command line option: nodisplay.
To get started, type doc.
For product information, visit www.mathworks.com.
Warning: Name is nonexistent or not a directory: C:\mnt\c\Users\maryk\MRI\fix
> In path (line 109)
In addpath (line 86)
Unrecognized function or variable 'fix_1a_extract_features' for input arguments of type 'char'.
Harms, Michael
Hi,
We have a separate pipeline for processing the ASL data from HCP-Lifespan.
And we have already processed the HCP-Lifespan data, which will be part of the “Release 3.0” at the NDA.
Cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
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
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Mary Huynh
Elam, Jennifer
Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
el...@wustl.edu
www.humanconnectome.org
Sent: Monday, February 10, 2025 3:21 PM
To: HCP-Users <hcp-...@humanconnectome.org>
Cc: Harms, Michael <mha...@wustl.edu>
Subject: Re: [hcp-users] ICA Fix processing
Mary Huynh
Harms, Michael
Also, it’s been incorporated into the QuNex container:
https://qunex.readthedocs.io/en/latest/wiki/UsageDocs/RunningHCPASL.html
--
Michael Harms, Ph.D.
-----------------------------------------------------------
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
Tim Coalson
Glasser, Matthew
Spatial ICA was tried on the ASL data, but it was difficult to separate signal and artifact components because there are so few timepoints in the ASL data.
Matt.
From:
Tim Coalson <tim.c...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Monday, February 10, 2025 at 5:52 PM
To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Cc: "Elam, Jennifer" <el...@wustl.edu>, "Harms, Michael" <mha...@wustl.edu>
Subject: Re: [hcp-users] ICA Fix processing
The question being answered in that quote was how to get an MSMAll-registered version of a file. MSMAll uses functional data (not ASL) for the alignment, and those requirements are for processing the functional data (so that MSMAll can be run). We do not run functional (aka BOLD, fMRI) pipelines on ASL data itself.
Tim
On Mon, Feb 10, 2025 at 4:39 PM Mary Huynh <maryki...@gmail.com> wrote:
Thank you Jennifer,
I saw a thread earlier that mentioned hcp_asl relies on the HCP pipeline. One of the responses said that you'd need to run Ica Fix (attached a screenshot). So wouldn't I still need to fix the errors I am getting on IcaFixProcessingBatch.sh?
Mary
