Dear Daniel,
I notice that your --field name has the extension .ni.gz. Should that maybe be .nii.gz?
Jesper
> On 30 Oct 2018, at 20:01, Daniel Callow <[log in to unmask]> wrote:
>
> So when I run this script (fixed the / issue)
> @ linenum = 1
>
> foreach subj (`ls -d /Volumes/DANIEL/AES102 | sed 's/\// /g' | awk '{print $3}'`)
>
> foreach cond (Rest)
>
> echo "subj = " ${subj} ", cond = " ${cond}
>
> cd /Volumes/DANIEL/${subj}/${subj}.${cond}
>
> #eddy correct function by fsl (on other computers probably needs to be eddy_openmp)
> #input origional dti dataset, binary mask that has been automatically and manually edited, acqp (text file/get from mri tech), index (text file), bvecs, and bvals.
> #replace outliers (--repol), output as eddy_corrected_data
> eddy --imain=DTI_analysis.nii.gz --mask=COPY_b0_brain_0.4_mask_eroded.nii.gz --acqp=acqp.txt --index=index.txt --bvecs=bvec.txt --bvals=bvalue.txt --repol --field=/Volumes/DANIEL/${subj}/${subj}.${cond}/field_map/FieldMap2dti.ni.gz --out=eddy_corrected_data
>
>
>
> end
>
> end
>
> I get [hlhp-105:DANIEL/scripts/5] administrator% ./script_eddy.sh
> subj = AES102 , cond = Rest
> eddy: msg=Error when attempting to read --field file
> libc++abi.dylib: terminating with uncaught exception of type EDDY::EddyException: eddy: msg=Error when attempting to read --field file
> Abort
>
> But when I remove the --field=.... portion out of my code it runs. So the issue is with reading the --field file?
>
>
> I checked to make sure it is indexing to the field map file correctly
>
> [hlhp-105:DANIEL/scripts/5] administrator% cd /Volumes/DANIEL/AES102/AES102.Rest/field_map/FieldMap2dti.nii.gz
> /Volumes/DANIEL/AES102/AES102.Rest/field_map/FieldMap2dti.nii.gz: Not a directory.
> [hlhp-105:DANIEL/scripts/5] administrator% cd /Volumes/DANIEL/AES102/AES102.Rest/field_map/
> [hlhp-105:AES102/AES102.Rest/field_map] administrator% ls
> FieldMap2dti.nii.gz
>
> Any idea why this issue might be persisting?
>
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