As i understand it, the dwell time in FUGUE is equal to the echo spacing, is that right ?
does a value of 0.7 seems right to you ? (echo spacing calculated for Philips data)
Thank you for your help
Christophe
________________________________________
De : FSL - FMRIB's Software Library [[log in to unmask]] de la part de Jesper Andersson [[log in to unmask]]
Envoyé : lundi 1 juin 2015 12:20
À : [log in to unmask]
Objet : Re: [FSL] FUGUE DTI Distorsion correction
Dear Christophe,
I am afraid that FUGUE and topup use different conventions. The dwell time (that is used in FUGUE) is the time between centres of consecutive echoes. So typically a factor ~100 or so smaller than the total readout time.
Jesper
On 1 Jun 2015, at 09:18, Maggia, Christophe <[log in to unmask]> wrote:
> 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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