That isn't the cause of that. If you want to restrict tracts to be within
the brain you need to use a stop mask of non-brain tissues (see previous
posts on the list about this).
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Francis Wong
Sent: Tuesday, October 12, 2010 11:07 AM
To: [log in to unmask]
Subject: Re: [FSL] averaging prob tracks DTI
Hi Jesper,
Yes it helps! thanks.
About the transformation in probtrackx, is there a way to specify the
interpolation method used to transform the tracking results back to MNI
space? There are some tracks spilled outside the brain, and I wonder if
this is due to a sub-optimal interpolation.
Thanks,
Francis
On Tue, 12 Oct 2010 12:30:28 +0100, Jesper Andersson <[log in to unmask]>
wrote:
>Hi Matt and Francis,
>
>> Okay, I don't know how FNIRT handles an --aff argument, if it
>> automatically
>> incorporates that into the resulting warp or not. Perhaps Jesper or
>> Mark
>> knows?
>
>I'm sorry I missed the initial part of this thread. fnirt includes the
>initial affine transform into its output (-cout) file. Applywarp knows
>this and extracts the affine warp from the header and combines that
>with the non-linear warps given by the coefficients.
>
>Hope that answers your question?
>
>Jesper
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.
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