Just so that people aren't confused - these two answers are
equivalent (applywarp and flirt can both do this resampling).
However, if your atlas image contains label values as
integers then it is better to do as Jesper says and use the
nearest neighbour interpolation when upsampling. Also, you
can find an identity matrix in $FSLDIR/etc/flirtsch/ident.mat
All the best,
Mark
On 29 Aug 2011, at 15:46, Jesper Andersson wrote:
> Dear Anna,
>
>> Thanks for your response. I am basically trying to use the AAL Atlas parcellation scheme for tractography on FA maps that have been normalized to the FMRIB58 1mm template. However, the AAL Atlas is defined in the 2mm T1 template and I can't open it on the 1mm FA or T1. Originally, I was thinking that I could flirt and fnirt the 2mm T1 template to the 1mm FA and then apply the resulting warp to the AAL Atlas. However, if you're saying that fnirt is unnecessary and that I shouldn't normalize between FA and T1 templates, would I be better off simply flirting the MNI152 T1 2mm template to the MNI152 T1 1mm template and then applying this warp to the atlas so that I can use it for tractography?
>>
>
> create a text file called eye.mat that contains the unity transform, i.e.
>
> 1 0 0 0
> 0 1 0 0
> 0 0 1 0
> 0 0 0 1
>
> and then run
>
> applywarp --ref=my_1mm_scan --in=my_2mm_roi --premat=eye.mat --out=my_1mm_roi -s --interp=nn
>
> which should do the trick.
>
> Good luck Jesper
>
>
>> Thanks in advance,
>> Anna
>>
>
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