Thank you! I figured out what I was doing wrong for indexing to the phase map image and magnitude image. However, it seems what I have for the output image isn't an acceptable input?
@ linenum = 1
foreach subj (`ls -d /mnt/e/AES101 | sed 's/\// /g' | awk '{print $3}'`)
foreach cond (Ex Rest)
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}.${cond}/phase_map/phase_map*.nii /mnt/e/${subj}/${subj}.${cond}/field_map_average/*eroded.nii prepared_fmap_rads.nii 2.46 --nocheck
I am getting this error
DESKTOP-U4H41O9:/mnt/e/scripts/2/field_map> ./fsl_prepare_fieldmap.sh
subj = AES101 , cond = Ex
prepared_fmap_rads.nii not found/not an image file
subj = AES101 , cond = Rest
prepared_fmap_rads.nii not found/not an image file
Thanks again for the previous advice!
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