For FLAIR you might be best off registering with a mean diffusion weighted
image (mean across all b=1000 or whatever direction images).
Peace,
Matt.
On 8/17/18, 8:24 AM, "FSL - FMRIB's Software Library on behalf of C.
Roman" <[log in to unmask] on behalf of [log in to unmask]> wrote:
>Dear Team FSL,
>
>I came across the below post while trying to find suggestions for a
>transformation I want to run. Do the same rules apply if I am trying to
>transform a T2 FLAIR into diffusion space. Originally, I was going to try
>to transform the T2 to b0 space, but after reading the message board, it
>appears that using the FA map is the better option?
>
>To give you a bit more context, I am looking to:
>
>1. Transform T2 FLAIR into diffusion space (i.e., b0 or FA map)
>
>2. Use the transformation matrix from (1) to move a binary lesion mask
>into diffusion space.
>
>Thanks in advance for your time and wisdom!
>Cristina
>
>
>__________________________________________________________________________
>___________________
>
>Hi again Anastasia,
>
>I played a little with your data, and the following strategy seems to work
>alright.
>
>#
># Erode FA image to get rid of bright edge.
>#
>fslmaths dti_FA.nii.gz -kernel 3D -ero eroded_FA
>
>#
># Crop T1-file to reduce FOV to where there is brain.
>#
>
>fslroi s03-2.3danat_flip_brain cropped_T1 14 140 45 180 40 145
>
>#
># Register FA image to T1 image. Intuitively this would make sense
># since we want to be in undistorted space, i.e. in T1 space.
># Note that the associated .cnf file
># a. Considers zero as "missing value" in both --ref and --in
># b. Ends with subsampling 2 since the ~1mm res in the T1 is overkill
>#
>
># Start with finding an affine transform
>flirt -ref cropped_T1 -in eroded_FA -omat FA_2_T1_Affine -out
>for_checking_how_it_went
># And non-linear
>fnirt --config=FA_2_same_subject_T1 --aff=FA_2_T1_Affine --ref=cropped_T1
>--in=eroded_FA --cout=FA_2_T1_warpcoef --iout=FA_warped_2_T1
>
>where I have attached the .cnf file to this mail. The crucial thing here
>(I think) is that by eroding the FA image I have removed the rim of high
>values.
>
>When looking at the warped FA image, it looks like it has done a quite
>good job of correcting the distortions without introducing any new ones
>(which would be a concern).
>
>Note that if you want the "warped" version of the original FA (with the
>rim intact) you need to run applywarp with the field you obtained above on
>a cropped (to get same FOV) version of the FA image.
>
>Having said that, this is NOT what fnirt is really written for. The fact
>that it happens to work is just a side effect of the intensity modelling,
>and I strongly suspect that this particular application will always be a
>bit "hit and miss" and that one will frequently have to resort to "little
>fixes" like the one above.
>
>The better approach to correcting distortions is to use fieldmaps to
>correct all the dwi's before further processing.
>
>Good luck Jesper
>
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