Hi Matt
Thank you for your quick response
the dwell time is in second
i modified the parameter of the brain extraction to adapt it better at my images
and i think the registration result with flirt are weird
when i look at the output of the first flirt on the magnitude image, it looks like noise...
and on the output of the second flirt (fieldmap), is also very deformed (brain compressed in two slice dimensions)
Thanks again
Christophe
________________________________________
De : FSL - FMRIB's Software Library [[log in to unmask]] de la part de Matt Glasser [[log in to unmask]]
Envoyé : vendredi 29 mai 2015 18:03
À : [log in to unmask]
Objet : Re: [FSL] FUGUE DTI Distorsion correction
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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