[Simnibs-discuss] Any way to match T2 FOV instead of T1 for charm?

[Oula Puonti]

Hi Brownyn,

charm resamples everything to the space of the first input image, so
technically you could run the pipeline with the T2 as the first input
at T1 as the second input. That would unfortunately flip your filenames
(T1.nii.gz being the T2, etc.), so maybe a better option would be to
run only the --registerT2 step first, i.e.,

charm <subid> <t2_image> <t1_image> --registerT2

and then grab the T1.nii.gz and T2_reg.nii.gz (which will now have
wrong names) and then re-run charm with those scans (passing them in
again in the expected order, i.e., T1 first and T2 second).

There's one caveat though: doing the above is a bad idea if the
resolution of your T2 is much lower than the resolution of your T1,
because the T1 will get resampled to the space of the T2. If that's the
case I would rather zero pad the T1 to extend the FOV.

Best,
Oula



On Thu, 2023-03-30 at 10:15 +0000, Bronwyn Gavine wrote:
> Hello simnibs team, 
>  
> Thank you for all the hard work you put into this great tool!
>  
> I have a dataset that includes T2 images with a large FOV (nose
> included) and T1 images with a tighter FOV. In a few subjects, the T1
> FOV is missing a part of the frontal scalp. I attach an image to show
> the difference in FOV between the tissue labelling volume and T2. 
> Is there any way to manually add in (rather than reclassify) extra
> tissue to the tissue_labeling_upsampled.nii.gz volume? Or any way to
> enlarge the T1 FOV to match the T2 FOV at the charm stage?
>  
> Would be grateful for any pointers!
>  
> Thanks very much. 
>  
> Warm regards, 
> Bronwyn
>  
> …….
> Dr Bronwyn Gavine
> MBChB (UCT) MSc Neuroscience (Oxon)
> Doctoral Candidate - Nuffield Department of Clinical Neurosciences
> University of Oxford
>  
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