I am having trouble running the following fsl_prepare_fieldmap
foreach subj (`ls -d /mnt/e/AES101 | sed 's/\// /g' | awk '{print $3}'`)
foreach cond (Ex)
echo "subj = " ${subj} ", cond = " ${cond}
cd /mnt/e/${subj}/${subj}.${cond}/
# Prepares a fieldmap suitable for FEAT from SIEMENS data - saves output in rad/s format
# Example: fsl_prepare_fieldmap <scanner> <phase_image> <magnitude_image> <out_image> <deltaTE (in ms)> [--nocheck]
fsl_prepare_fieldmap SIEMENS /mnt/e/${subj}/${subj}.${cond}/phase_map*.nii /mnt/e/${subj}/${subj}.${cond}/field_map_average/*eroded.nii prepared_fmap_rads.nii 2.46 --nocheck
I get the output
DESKTOP-U4H41O9:/mnt/e/scripts/2/field_map> ./fsl_prepare_fieldmap.sh
subj = AES101 , cond = Ex
fsl_prepare_fieldmap: No match.
Is it okay to index to the files the way I have for my fsl_prepare_fieldmap? It seems like there is an issue with the imputs.
Thanks for any advice you can provide!
Daniel Callow
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