Hi,
In most cases the answer is yes:
(i) all segmentations are in native space;
(ii) it makes sense to transform results into MNI space to account for head-size, however this should be done with the linear transformation and not the non-linear transformation, as in the latter case you will remove some of the biological/pathological change itself. The option useReconMNI in vertex analysis only uses the linear transformation. You can use applywarp to transform to MNI space, but you should _not_ use the warp field, but use the linear transformation matrix (with --premat).
I hope this is clear.
All the best,
Mark
> On 19 Sep 2018, at 12:54, Therese Gilligan <[log in to unmask]> wrote:
>
> Hello,
>
> I have a query regarding the outputs of fsl_anat from fsl version 5.0.8.
>
> Following fsl_anat the partial volume estimates are in native space. Are the subcortical volumes also calculated from native space?
>
> I am comparing controls to a disease group, is there any value in transforming both outputs into nonlinear jacobian space? If yes, is it possible/does it make sense to use ‘applywarp’ function on a T1_first_all_fast_firstseg.nii file?
>
> Likewise, is there a value in performing shape (vertex) analysis in nonlinear jacobian space? If yes, would I use the –r argument in first_utils to call the jacobian image alongside the –useReconMNI argument?
>
> Many thanks in advance for your help.
>
> Therese
>
> ########################################################################
>
> To unsubscribe from the FSL list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
|