I think some of your subjects are not registered correctly in that case, as
that is quite far off.
Peace,
Matt.
-----Original Message-----
From: Francis Wong [mailto:[log in to unmask]]
Sent: Thursday, October 14, 2010 4:05 PM
To: [log in to unmask]; Matt Glasser
Subject: Re: averaging prob tracks DTI
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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