It looks like this (in the attachment), although the values are small.
Thanks,
Francis
On Tue, 12 Oct 2010 11:15:06 -0500, Matt Glasser <[log in to unmask]> wrote:
> 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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