[MINC-users] Best plane (axial or coronal) for CIVET processing?

[Alex Zijdenbos]

Hello Kie Woo,

Are you referring to two images _acquired_ in different orientations
(i.e., two different acquisitions), or two images simply (re)sampled
(or reshaped) to have different dimension ordering? In the latter case
you really should obtain identical results (unless you changed voxel
sizes or manipulated the data in some other way); so I assume you are
talking about the former, i.e., you have two different acquisitions.
In this case you would expect to get slightly different results -
there is an inherent scan-rescan variability associated with any type
of image processing tool, simply because the image you provide is a
different one. In other words, if you would take two axial or two
coronal scans acquired in sequence, you would also see a difference in
image processing results.

The only reason I can think of why coronally scanned data would yield
more or less accurate results as compared to axial images is if there
is a difference in the image quality, in terms of intensity uniformity
for example. Otherwise I would say the results should be equivalent.
Being consistent however is always good; for example, I would
definitely not change your acquisition protocol in the middle of a
longitudinal study, if that is what you are contemplating.

-- Alex

On Sun, Mar 18, 2012 at 2:07 PM, Nam, Kie Woo <kie_woo.nam at kcl.ac.uk> wrote:
> Dear experts,
>
> I know this mailing list is not particularly for CIVET pipeline, but could someone please advise me the best plane (axial or coronal) for images to be in for CIVET processing?
>
> I've recently run CIVET on an image in coronal and axial planes (i.e. 2 identical images just in different planes), and noticed that the outputs differed. This was noticeable in the "clasp" images as well as the text files (example shown below).
>
> ...brainmask_qc.txt
>
> Axial image: native skull mask in stx space (10.83%)
>
> Coronal image: native skull mask in stx space (11.96%)
>
> My original images were in coronal plane, so I'm thinking of doing CIVET processing on coronal images. However, I'm not convinced whether this is a good choice. So, if anyone would please advise me on this, I would much appreciate it.
>
> Best wishes,
>
> Kie Woo
>
> Kie Woo Nam
> Postgraduate Research Student
> Division of Psychological Medicine
> Department of Psychosis Studies
> Institute of Psychiatry, King’s College London
> De Crespigny Park, Denmark Hill
> London SE5 8AF, UK
> Tel: +44 (0)20 7848 0061
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