Hi Tim,
Below, I am copying both the error and the script.
Thank you so much for your help!
Best,
Levi
*Error:*
The precise error I'm getting is:
DiffPreprocPipeline_PreEddy.sh - PosInputImages:
$/projects/IndivRITL/data/leviDiff/disk1/128632/unprocessed/3T/Diffusion/128632_3T_DWI_dir95_RL.nii.gz
$/projects/IndivRITL/data/leviDiff/disk1/128632/unprocessed/3T/Diffusion/128632_3T_DWI_dir96_RL.nii.gz
$/projects/IndivRITL/data/leviDiff/disk1/128632/unprocessed/3T/Diffusion/128632_3T_DWI_dir97_RL.nii.gz
ERROR: Could not open file
Usage: /usr/local/fsl/bin/imcp <file1> <file2>
Usage: /usr/local/fsl/bin/imcp <file1> <file2> ... <fileN> <directory>
Copies images from file1 to file2 (including all extensions)
*This is my script:*
#!/bin/bash
#source opts.shlib
#Diffusion preprocessing for the HCP Data
#get_batch_options $@
#Script for running this on the supercomputer
StudyFolder="$/projects/IndivRITL/data/leviDiff/disk1" #Location of Subject
folders (named by subjectID)
Subjlist="108121" #Space delimited list of subject IDs #Pipeline
environment script
HCPPipe="/usr/local/HCP_Pipelines"
EnvScript="${HCPPipe}/Examples/Scripts/SetUpHCPPipeline.sh"
#Set up pipeline environment variables and software
. ${EnvScript} #sets up the pipeline environment
# Log the originating call
echo "$@"
for Subject in $Subjlist ; do
echo $Subject
EchoSpacing=0.78
PEdir=1 #Use 1 for Left-Right Phase Encoding, 2 for Anterior-Posterior
#Input Variables
SubjectID="$Subject" #Subject ID Name
RawDataDir="$StudyFolder/$SubjectID/unprocessed/3T/Diffusion/" #Folder
where unprocessed diffusion data are
# Data with positive Phase encoding direction. Up to N>=1 series (here
N=3), separated by @. (LR in HCP data, AP in 7T HCP data)
PosData="${RawDataDir}/${SubjectID}_3T_DWI_dir95_RL.nii.gz@
${RawDataDir}/${SubjectID}_3T_DWI_dir96_RL.nii.gz@
${RawDataDir}/${SubjectID}_3T_DWI_dir97_RL.nii.gz"
# Data with negative Phase encoding direction. Up to N>=1 series (here
N=3), separated by @. (RL in HCP data, PA in 7T HCP data)
NegData="${RawDataDir}/${SubjectID}_3T_DWI_dir95_LR.nii.gz@
${RawDataDir}/${SubjectID}_3T_DWI_dir96_LR.nii.gz@
${RawDataDir}/${SubjectID}_3T_DWI_dir97_LR.nii.gz"
#Scan Setings
#EchoSpacing=0.78
#PEdir=1 #Use 1 for Left-Right Phase Encoding, 2 for Anterior-Posterior
Gdcoeffs="NONE" # Set to NONE to skip gradient distortion correction
echo "About to run
${HCPPIPEDIR}/DiffusionPreprocessing/DiffPreprocPipeline.sh"
queuing_command=""
${queuing_command}
${HCPPIPEDIR}/DiffusionPreprocessing/DiffPreprocPipeline.sh \
--posData="${PosData}" --negData="${NegData}" \
--path="${StudyFolder}" --subject="${SubjectID}" \
--echospacing="${EchoSpacing}" --PEdir=${PEdir} \
--gdcoeffs="${Gdcoeffs}" \
--printcom=$PRINTCOM
done
On Mon, Jun 22, 2015 at 1:53 PM, Timothy B. Brown <[email protected]> wrote:
> Hi Levi,
>
> Yes, it would be helpful in investigating the error you are receiving to
> see both the script you are running and a capture of the exact output you
> are getting from a run of the script. That output might help to determine
> if the "ERROR: could not open file" being reported by the imcp command is
> because it cannot find the file that it is supposed to copy or because it
> cannot open/create the file it is supposed to be creating as a copy.
>
> Thanks,
> Tim
>
> On Thu, Jun 18, 2015, at 14:32, levi solomyak wrote:
>
> Hello,
>
> I am working on running the diffusion preprocessing pipeline using the
> script from
> https://github.com/Washington-University/Pipelines/blob/master/Examples/Scripts/DiffusionPreprocessingBatch.sh
> as a reference.
>
> When it is supposed to copy the positive raw data to the working directory
> I keep getting an ERROR: could not open file (for the imcp command). The
> files themselves are not corrupted, and imcp works, and I checked that my
> StudyFolder path and EnvScript are correct. I am new to preprocessing HCP
> data so its very possible that I'm missing something basic.
>
> Does anyone know how to fix this kind of issue? I would be happy to
> provide my script for reference.
>
> Thank you so much!
> Levi Solomyak
>
>
>
> _______________________________________________
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> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
> --
> Timothy B. Brown
> Business & Technology Application Analyst III
> Pipeline Developer (Human Connectome Project)
> tbbrown(at)wustl.edu
> ________________________________________
> The material in this message is private and may contain Protected
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> If you are not the intended recipient, be advised that any unauthorized
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>
--
Levi Solomyak
Cole Neuroscience Laboratory (*colelab.org <http://colelab.org/>*)
Center for Molecular and Behavioral Neuroscience (CMBN)
Rutgers-Newark University
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