Combining deformations enables you to skip creating the warped
images---your step 7. Instead the flow fields are combined with the
Template*_sn.mat information so that images can be brought from their
original orientation to MNI space in a single step. If this is all
you need, you could skip your step 7
> 7) Create warped - specify u_rc1ms*.nii, rc1ms*.nii, and rc2ms*.nii
> files; select "modulation", 64 time steps, trilinear interpolation.
> Produces mwrc1ms*.nii and mwrc2ms*.nii
> 8) Affine transform of DARTEL template to MNI space (1.2.1 in DARTEL
> guide), using all options detailed in the guide
This is in the right place---any time after the template is created.
> 9) Combine deformations (1.2.2 in guide), using options detailed in
> guide. Apply to mwrc1ms*.nii and mwrc2ms*.nii for each subject,
> produces wmwrc1ms*.nii and wmwrc2ms*.nii
This is in the right place; however, you will want to apply the
combined deformations to the non-normalized images. In other words,
rc1* rather than mwrc1*, as the mw* images already have one of the
deformations applied, and you are aiming to do everything in a single
One thing to keep in mind with the combined deformations is, as far as
I know, these images are not modulated, which will affect
interpretation of the results.
> I have segmentation run twice, once to produce the bias corrected
> image and another to segment the bias corrected image. This comes
> after reading John's response to the "unified segmentation and bias
> correction - two steps?" question. If I have misinterpreted the
> solution suggested by John, please let me know.
Sounds like you're doing it right.
> can I
> change the GM and WM output files from "Native Space" to "none" to
> save time?
Yes, all you need from the first step is the bias-corrected structural.
Hope this helps. Good luck!