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

[Alex Zijdenbos]

I can take a stab at this - Andrew can correct me if I am wrong somewhere.

>From the 'register' screenshot I would say that the image on the left
(I assume that is the 'axial') is converted correctly (barring a
left-right inversion that wouldn't be visible); and the second one is
incorrectly converted.

I suspect that nii2mnc (or ana2mnc) has no way of knowing that you
flipped the axes around, so it converts the image the same way for
both images. You can probably fix this by providing ni2mnc with one of
the spatial dimension ordering options, such as -coronal, to tell it
what the ordering of the dimensions in your image is.

Be aware though of left-right inversions; I have seen many cases where
the left and right sides are inverted in converting from "unaware"
image formats to an "aware" format such as MINC. If you can you should
always double check the sidedness; most brains are asymmetric enough
to allow you to verify the sides. All MINC tools display data in
neurological convention (left=left).

-- A

On Thu, Mar 22, 2012 at 2:35 PM, Nam, Kie Woo <kie_woo.nam at kcl.ac.uk> wrote:
> Dear Dr Andrew Janke,
>
> Thank you very much for this precious information. The reason why I've been
> using "ana2mnc" was just that it came up on top of the google search results
> list.
>
> Anyway, I've now used "nii2mnc", and have further questions. So, I would
> very much appreciate your further advice.
>
>
>
>
> I've checked that the axial and coronal MINC images do not align when loaded
> using "register" (shown in attached the image) even though both the coronal
> and axial images have the same (1) messages displayed on terminal during
> nii2mnc conversion, (2) "mincheader" outputs and (3) "mincstats" outputs
> (shown in attached the Excel sheet).
>
>
>
>
> So, could you please tell me whether the nii2mnc conversion has been done
> properly? If not, I would be grateful if you would advise me on how to fix
> this. Please be reminded that my interest is not in having both axial and
> coronal MINC images, but just making sure the UNC-to-Analyze-to-MNC has been
> done successfully whether it's is in axial or coronal plane.
>
> Many thanks,
>
> Kie Woo
>
>
> ________________________________________
> From: minc-users-bounces at bic.mni.mcgill.ca
> [minc-users-bounces at bic.mni.mcgill.ca] on behalf of Andrew Janke
> [a.janke at gmail.com]
> Sent: 21 March 2012 20:09
>
> To: MINC users mailing list
> Cc: Simmons, Andy
>
> Subject: Re: [MINC-users] Best plane (axial or coronal) for CIVET
> processing?
>
> Hi all,
>
> On 22 March 2012 04:07, Nam, Kie Woo <kie_woo.nam at kcl.ac.uk> wrote:
>> ana2mnc: No x origin info found, guessing..
>> ana2mnc: No y origin info found, guessing..
>> ana2mnc: No z origin info found, guessing..
>>
>> Anyway, thanks to your clarification, my concern is not about whether to
>> use axial or coronal images any more. Instead, I now wish to check whether
>> the "ana2mnc" worked correctly.
>
> I'm curious as to why you are using ana2mnc and not nii2mnc? nii2mnc
> is part of MINC itself and can handle both ANALYZE and Nifti-1 data.
> nii2mnc was written as a replacement to ana2mnc a while back.
>
>
> a
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