Hello everyone
I tried to correct distorsion from DTI images using FUGUE with a fieldmap
I followed the commands described in Matt's response :
"Here is some example code that I have used in the past to unwarp DTI data with a field map:
bet FieldMap/Magnitude.nii.gz FieldMap/Magnitude_brain.nii.gz -f .3 -m
fslmaths FieldMap/FieldMap.nii.gz -mas FieldMap/Magnitude_brain_mask.nii.gz FieldMap/FieldMap_brain.nii.gz
fugue --loadfmap=FieldMap/FieldMap_brain -s 4 --savefmap=FieldMap/FieldMap_brain_s4
fslroi DTI/data1.nii.gz DTI/nodif 0 1
eddy_correct DTI/data1.nii.gz DTI/data1_corr.nii.gz 0
bet DTI/nodif.nii.gz DTI/nodif_brain -m -f .3
fugue -v -i FieldMap/Magnitude_brain --unwarpdir=y --dwell=0.000720 --loadfmap=FieldMap/FieldMap.nii.gz -w FieldMap/Magnitude_brain_warpped
flirt -in FieldMap/Magnitude_brain_warpped.nii.gz -ref DTI/nodif_brain.nii.gz -out FieldMap/Magnitude_brain_warpped_2_nodif_brain -omat FieldMap/fieldmap2diff.mat
flirt -in FieldMap/FieldMap_brain_s4.nii.gz -ref DTI/nodif_brain -applyxfm -init FieldMap/fieldmap2diff.mat -out FieldMap/FieldMap_brain_s4_2_nodif_brain
fugue -v -i DTI/data1_corr.nii.gz --icorr --unwarpdir=y --dwell=0.000720 --loadfmap=FieldMap/FieldMap_brain_s4_2_nodif_brain.nii.gz -u data/data.nii.gz
"
I adapted it to my images, but at the end of the processus, the "corrected DTI image" is almost empty,
I have a fieldmap in rad/s, a Magnitude map and DTI images
the DTI dwell time is 0.0413
I do not understand why it does not work ...
Can you help me ?
if you want, i can upload these images...
Thanks
Christophe
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