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Hello everyone, I did not managed to make Fugue work with my fieldmaps yet... I think something go wrong when i try to use fugue on the magnitude map (magmap_brain) i joined some images of what i get (magmap_warped 1, 2 and 3) I tried every solution i could find I don't know if the problem comes from the field map acquired on the MRI or if i do something wrong with FSL Can someone help me, i don't know what to do thanks, Christophe ________________________________________ De : FSL - FMRIB's Software Library [[log in to unmask]] de la part de Matt Glasser [[log in to unmask]] Envoyé : mardi 2 juin 2015 18:19 À : [log in to unmask] Objet : Re: [FSL] FUGUE DTI Distorsion correction Maybe the field map isn’t prepared properly? I don’t know how to do it for a Philips scanner, but perhaps someone else does. Peace, Matt. On 6/1/15, 11:27 PM, "Maggia, Christophe" <[log in to unmask]> wrote: >Thank you Matt > >I modified my dwell time (0.0007 s) >I followed your previous message step by step, but it does not work. > >i think the warping of the magnitude map (Magmap) with FUGUE must go >wrong, because i get warped noise instead of a warped magnitude map... > > >Christophe >________________________________________ >De : FSL - FMRIB's Software Library [[log in to unmask]] de la part de >Matt Glasser [[log in to unmask]] >Envoyé : lundi 1 juin 2015 16:21 >À : [log in to unmask] >Objet : Re: [FSL] FUGUE DTI Distorsion correction > >Units are in seconds, value is tenths of milliseconds. > >Peace, > >Matt. > >On 6/1/15, 9:11 AM, "Maggia, Christophe" <[log in to unmask]> wrote: > >>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