IMCP error, HCP pipeline

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Kristian M Eschenburg

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Aug 25, 2021, 4:36:10 PM8/25/21
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Hi HCP

I'm running the HCP Pipeline GenericfMRIVolumeProcessingPipelineBatch.sh script on the Example subject data provided with the pipeline.

I'm running into this error:

"""
Wed Aug 25 13:13:32 PDT 2021:GenericfMRIVolumeProcessingPipeline.sh: ERROR: '/usr/local/fsl/6.0/bin/imcp' command failed with return code: 127

===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
         script: GenericfMRIVolumeProcessingPipeline.sh
stopped at line: 823
           call: ${FSLDIR}/bin/imcp "$fMRITimeSeries" "$fMRIFolder"/"$OrigTCSName"
  expanded call: /usr/local/fsl/6.0/bin/imcp /projects3/HCP_SampleData/100307/unprocessed/3T/rfMRI_REST1_RL/100307_3T_rfMRI_REST1_RL.nii.gz /projects3/HCP_SampleData/100307/rfMRI_REST1_RL/rfMRI_REST1_RL_orig
      exit code: 127
"""

Error code 127 generally means the script can't be found, but imcp is used in previous pipeline scripts.  When I try to run the expanded call itself, I see this repeating message:

"""
/usr/local/fsl/6.0/bin/imcp /projects3/HCP_SampleData/100307/unprocessed/3T/rfMRI_REST1_RL/100307_3T_rfMRI_REST1_RL.nii.gz /projects3/HCP_SampleData/100307/rfMRI_REST1_RL/rfMRI_REST1_RL_orig
bash: warning: shell level (1000) too high, resetting to 1
bash: warning: shell level (1000) too high, resetting to 1
bash: warning: shell level (1000) too high, resetting to 1
......
"""

Unsure what to do here -- any help is much appreciated.

Kristian

--
Kristian M. Eschenburg
ARCS Graduate Research Fellow
PhD Candidate | Department of Bioengineering
Integrated Brain Imaging Center | University of Washington

Coalson, Timothy Scott (S&T-Student)

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Aug 25, 2021, 4:41:26 PM8/25/21
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"shell level too high" sounds like it may have ended up in endless recursion rather than calling the binary executable.  Did anyone modify your fsl 6 directory after installation?

Tim

From: Kristian M Eschenburg <kesc...@uw.edu>
Sent: Wednesday, August 25, 2021 3:31 PM
To: hcp-...@humanconnectome.org <hcp-...@humanconnectome.org>
Subject: [hcp-users] IMCP error, HCP pipeline
 
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Glasser, Matt

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Aug 25, 2021, 5:03:29 PM8/25/21
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I see this is posted on FSL as well.  It would probably be a good idea to specify the FSL version and operating system over there.

 

Matt.

 

From: Kristian M Eschenburg <kesc...@uw.edu>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Wednesday, August 25, 2021 at 3:31 PM
To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Subject: [hcp-users] IMCP error, HCP pipeline

 

 

Hi HCP

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Kristian M Eschenburg

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Aug 25, 2021, 5:20:14 PM8/25/21
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Hi

We did apply this change from this previous thread to the FSL 6 directory, since we were having Numpy issues with imcp:



k


Glasser, Matt

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Aug 25, 2021, 5:23:56 PM8/25/21
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Since that was for FSL 6.0.4 and they said the issue would be fixed in the next FSL version, could you try upgrading to FSL 6.0.5?

 

Matt.

Coalson, Timothy Scott (S&T-Student)

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Aug 25, 2021, 5:53:48 PM8/25/21
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If 6.0.5 is not an option for some reason, double check the line:

$thisdir/python3.7_bin -I "$@"

If it doesn't have the "_bin" (which points to the python binary you should have renamed), it would error like this.

Tim

From: Glasser, Matt <glas...@wustl.edu>
Sent: Wednesday, August 25, 2021 4:23 PM

Kristian M Eschenburg

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Aug 25, 2021, 6:12:07 PM8/25/21
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Hi Matt and Tim

Thanks for the clarification -- we're using 6.0.3, so that explains the continued imcp issue.  Our machines will be upgraded to 6.0.5 next week.

You're correct about the endless recursion -- somehow we mistakenly overwrote both the python3.7 and python3.7_bin using the same script suggested by Paul in https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=FSL;a26a0779.2010 -- the end result being that neither python3.7 nor python3.7_bin pointed to a working python3.7 version.  Correcting this has fixed the problem.

Thank you!


k

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