Dear Nader,
>
> Any progress yet on getting FNIRT to register my 5 mm slice
> thickness diffusion data? Thanks,
as we discussed before the problem has to do with the thick slices
you are using. They are actually 7.5mm, rather than 5mm as I think we
thought before.
I would argue strongly against using a "study derived template".
Given your slice thickness the template will inevitably be of quite
poor quality. I would instead recommend you using the supplied
"standard template" by specifying the -T switch.
If you absolutely want to use one of your own scans as a template I
there are two possible ways forward. In the
FA_2_FMRIB58_1mm.cnf
configuration file you need to make sure that --warpres *
final_subsampling >= voxel_dim_of_your_template
In your case the critical dimension is z, where you have a voxel-size
of 7.5mm. One way to fulfill the criterion is to change the line
--warpres=10,10,10
to
--warpres=10,10,15
which means the criterion would be fulfilled. This is the option I
would recommend.
Your other option is to change
--subsamp=8,4,2,2
to
--subsamp=8,4,2,1
which would also mean you fulfill the criterion. I would _NOT_
recommend this.
Also, let me again say that my #1 recommendation for you is to use
the supplied standard FA-template, and not change the configuration
file.
Good Luck Jesper
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