Thanks! Do you know how I would install gradient_unwarp.py ?
On 25 Jul 2018, at 21:39, Glasser, Matthew wrote:
That error suggests the tool is not installed or not installed
correctly so it is available on the path.
Peace,
Matt.
From:
<[email protected]<mailto:[email protected]>>
on behalf of Marc Dubin
<[email protected]<mailto:[email protected]>>
Date: Wednesday, July 25, 2018 at 8:37 PM
To:
"[email protected]<mailto:[email protected]>"
<[email protected]<mailto:[email protected]>>
Subject: [HCP-Users] gradient_unwarp.py error
Hello All,
When trying to do the Gradient Distortion Correction in the
Pre-Freesurfer stage of the structural preprocessing, I get the
following error:
/home/mrd9035/projects/Pipelines/global/scripts/GradientDistortionUnwarp.sh:
line 89: gradient_unwarp.py: command not found
In the code, it says:
NB: gradient_unwarp.py must have the filename extensions written out
explicitly or it will crash
gradient_unwarp.py ${BaseName}_vol1.nii.gz trilinear.nii.gz siemens -g
$InputCoeffs -n
Which files need to have the filename extensions written? I’m
assuming this is the reason the pipeline is crashing at this stage for
me.
Thanks for any suggestions!
Marc
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