Hello List,
To combine DTI with VBM, I have now tried the following:
For each individual T1/DTI:
a) segment GM and WM (without custom priors, as I have an average population)
b) use DARTEL to create flow fields and rc1, rc2 images, to which flow
fields can/will be applied.
c) co-register & re-sample the FA images so that they match rc2 (white
matter). (On visual inspection, they match nicely...)
d) update the headers of rFA (using load_nii and save_nii) so that the
qform matrix matches that of the rc2 images (they are considered to be
'imported' in this way)
e) apply the warps, (do not modulate the rFA, modulate the rc2)
f) use the script normalize_DARTEL.m to change voxel dimensions so
that it more matches the NMI space.
g) smooth 8 mm^3.
i) apply statistics (with the swrFA.* images in "perfect" alignment
with the smwrc2.* images)...
I guess I resample the FA twice in this way, which could possibly
avoided. I was wondering if anyone sees any major issues in this
work-flow, or has suggestion on how to improve it. I did read the
article by Canu et. al.
To see if the flow-fields can be applied to co-registered FA (the FA
was acquired axial, and the t1 saggital, which worried me), I have
tried to figure out how to translate the sform and qform matrices of
the rc2*.nii images to the sform matrix of the (unimported) FA*.nii
images, but i couldn't figure out how to equate the sform of the FA*
to the sform of the rc2*.
Best regards,
Johan
On Fri, Dec 11, 2009 at 2:13 PM, Dr. Maximilian Wagner
<[log in to unmask]> wrote:
> Dear John,
>
> thank you for the suggestion. Just to double check: If I understand this
> correctly, DARTEL applies the second matrix (used for the alignment of the
> scans during the import step) to allow for the application of the flow field
> (e.g. estimated on T1 scans) to non-imported scans (e.g. DTI, fMRI) in the
> native space for highdimensional normalization, under the assumption that
> the original T1 scans and DTI/fMRI scans were collected in the same subject
> specific native space.
> Thus, if we apply the DARTEL flow fields with the "Dartel-Normalize-to-MNI"
> tool (without specifying template_6.nii) to non-imported DTI scans that were
> coregistered with imported GM segments (rc1 scans) rather than the "native"
> c1 scans, DARTEL would wrongly apply the combination of flow fields and the
> affine matrix to the DTI scans that are actually in the "inter-subject"
> rigidly aligned native space rather than the individual native space?
>
> Best regards,
> Max
>
>
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