It seems that what I am using for the output image for my fsl_prepare_fieldmap 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 get this error when running the script
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
Again, it seems like the command is having an issue with outputting the file? What do you think is causing this error?
Thanks for any help you can provide!
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