What are the units of that dwell time? Did all those brain extractions
and registrations produce reasonable results?
Peace,
Matt.
On 5/29/15, 7:41 AM, "Christophe Maggia" <[log in to unmask]> wrote:
>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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