I have a doubt ...
the dwell time is equal to the total readout time, right ? (like the one used in topup)
because i calculated it again and i obtain the same result.
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 18:52
À : [log in to unmask]
Objet : Re: [FSL] FUGUE DTI Distorsion correction
I don¹t think you¹ve got your dwell time correct, as typical values are in
the tenths of a millisecond.
Peace,
Matt.
On 5/29/15, 10:28 AM, "Maggia, Christophe" <[log in to unmask]> wrote:
>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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