That ended up working somewhat.
Now my code ....
@ linenum = 1
foreach subj (`ls -d /Volumes/DANIEL/AES119 | sed 's/\// /g' | awk '{print $3}'`)
foreach cond (Ex)
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/AES119/AES119.Rest/field_map/FieldMap2dti.nii.gz --out=eddy_corrected_data
end
end
gives me the output
[hlhp-105:DANIEL/scripts/5] administrator% ./script_eddy.sh
subj = AES121 , 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
Any ideas why it can't read the field map?
Thanks!
Daniel Callow
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