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

[Nam, Kie Woo]

Dear Alex,

I much appreciate your quick and detailed reply.

I find your advice very useful, but my image has been acquired only in the coronal plane in UNC format. I've converted it into Analyze format in coronal (using "unc2analyze") and axial (using "coronal2axial") planes. After that, I've converted both Analyze images into MNC format using "ana2mnc<http://packages.bic.mni.mcgill.ca/scripts/ana2mnc-1.3d>".

I've compared the axial and coronal Analyze images and checked that the signal intensities were the same in a few randomly picked voxels. I couldn't check the MNC images properly because of difficulty selecting exact same voxels in both images (using MNC viewing software like "Display" and "register"), but I couldn't tell any visual difference between the axial and coronal MNC images.

Anyway, thank you very much again for your advice. For now, I'll just stick to the images in the original (i.e. coronal) plane.

Best wishes,

Kie Woo



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Message: 1
Date: Sun, 18 Mar 2012 18:07:21 +0000
From: "Nam, Kie Woo" <kie_woo.nam at kcl.ac.uk>
Subject: [MINC-users] Best plane (axial or coronal) for CIVET
processing?
To: "minc-users at bic.mni.mcgill.ca" <minc-users at bic.mni.mcgill.ca>
Cc: "Simmons, Andy" <andy.simmons at kcl.ac.uk>
Message-ID:
<194921E98A6CEC41B0C14C804A56CC90CFF0B4 at DBXPRD0310MB382.eurprd03.prod.outlook.com>

Content-Type: text/plain; charset="Windows-1252"

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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Message: 2
Date: Sun, 18 Mar 2012 17:43:20 -0400
From: Alex Zijdenbos <zijdenbos at gmail.com>
Subject: Re: [MINC-users] Best plane (axial or coronal) for CIVET
processing?
To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
Message-ID:
<CABEEk15OETNOP61yqqVbDn0zTRxLOub16FsrJ3nB9ETEtc8utw at mail.gmail.com>
Content-Type: text/plain; charset=windows-1252

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
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


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End of MINC-users Digest, Vol 80, Issue 9
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