1) Yes you do. Specify it as a premat if you are using applywarp on the
forward warp or as a postmat if you are using applywarp on the inverse warp.
If you are going to be using --xfm --invxfm, you need to concatenate it to
the warp. You can do this with convertwarp (specify it as a premat). Then
invert the resulting warp (or you could concatenate it as a premat on the
forward warp and as a postmat on the inverse warp if you don't want to run
invwarp again).
2) It looks like you are not using the correct reference volume for the
second apply warp step. That should be dti_FA.nii.gz
3) Yes it does, unless Saad is playing a cruel trick on us all...
Peace,
Matt.
-----Original Message-----
From: Francis Wong [mailto:[log in to unmask]]
Sent: Monday, October 11, 2010 11:56 AM
To: [log in to unmask]; Matt Glasser
Subject: Re: averaging prob tracks DTI
Hi Matt,
I am trying to perform what you have suggested, to apply the non-linear
transform obtained from TBSS to transform an ROI defined in MNI space to a
subject's native diffusion space for probtrackx. I would like to make sure
if I am doing it right. Many thanks in advanced.
From the outputs of TBSS, for each subject we have the warp field
(FA_to_target_warp.nii.gz) and the affine transform
(target_to_FA.mat)
then I did
invwarp --warp=FA_to_target_warp.nii.gz --out=target_to_FA_warp
--ref=FMRIB58_FA_1mm.nii.gz
to get the non-linear transformed needed to put the ROI to the subjects'
native diffusion space.
and here are my questions:
1) Do we need to care about the affine transform anymore? That is, when
doing the applywarp, do we need to put it as --premat or --postmat?
2) I performed the applywarp twice to check if the transform works:
applywarp --ref=FMRIB58_FA_1mm.nii.gz --in=dti_FA.nii.gz
--warp=FA_to_target_warp.nii.gz --out=warpped_FA
applywarp --ref=FMRIB58_FA_1mm.nii.gz --in=warpped_FA.nii.gz
--warp=target_to_FA_warp.nii.gz --out=re-warpped_FA
while the warpped_FA matches the FMRIB58 very well, the re-warpped_FA does
not match the subject's native FA image that a large portion of it was
cropped. also, the dimension of the re-warpped_FA does not match the
original dti_FA. Something must be wrong in the process.
3) Does probtrackx really accept the warp fileds as --xfm and --invxfm? Cos
in fdt_gui, there is no such option to perform a non-linear transform.
Thanks,
Francis
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