[MINC-users] mnc2nii and mnc2ana

[Søren Christensen]

Hi Bert,
 Cheers, with this kind of help i will never use a commercial program again..
It works perfectly.

Thanks!

Soren



-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Robert VINCENT
Sent: Wed 19-10-2005 11:17
To: MINC users mailing list
Subject: Re: [MINC-users] mnc2nii and mnc2ana
 
Hi Soren,

I think I understand what is happening with mnc2nii...

First off, we generally have to map the MINC information into a form NIfTI
and Analyze can handle. This means that we have to set step sizes to a
positive value and rearrange the data appropriately. There's no real way
around this.

You have found a bug, however. There is a field named "spacetype" which is
supposed to be set in the MINC header, and this guides the conversion to
.NII format.  This field is normally set to the value "native____". The
problem is that when I wrote the code I do not handle the situation where
the field is not set at all, and so we discard the MINC header spatial
information. This is why the transform in the header is wrong

I'll put a fix for this into the next version.  In the meantime, I would
recommend that you try setting the field in the header of the file you'd
like to convert and see if that helps:

minc_modify_header -sinsert zspace:spacetype="native____" sel.mnc

Try the conversion again after making this adjustment.

Sorry for the complication,

	-bert


On Wed, 19 Oct 2005, Søren Christensen wrote:

> Hi,
>  I am having trouble using mnc2nii and mnc2ana.
> I run:
>  mnc2nii se1.mnc se.nii
>  nii2mnc se.nii se1n.mnc
>
> and mincinfo gives:
>
> file: se1.mnc
> image: signed__ short 0 to 1462
> image dimensions: zspace yspace xspace
>     dimension name         length         step        start
>     --------------         ------         ----        -----
>     zspace                     19            7        -47.3
>     yspace                    256    -0.859375       101.87
>     xspace                    256    -0.859375       109.57
>
>
> file: se1n.mnc
> image: signed__ float 0 to 1026
> image dimensions: zspace yspace xspace
>     dimension name         length         step        start
>     --------------         ------         ----        -----
>     zspace                     19            7        -66.5
>     yspace                    256     0.859375         -110
>     xspace                    256     0.859375         -110
>
>
> I was wondering if someone has an explanation. The version is:
>
> mnc2nii -version
> program: 1.4
> libminc: 1.4
> netcdf : 3.6.0-p1 of Jun 10 2005 16:14:06 $
>
>
>
> When doing the same back and forth procedure with mnc2ana descrepancies in step and start also arises. Spatially, mnc2nii -> nii2mnc throws the scan a bit off position while mnc2ana -> ana2mnc flips the x-axis and also change the start points numerically.
>
>
>
> If anyone has a good way of using FSL's BET with MINC i'd be interested to hear about it!
>
>
>
>
>
> Best regards
> Soren
>
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>


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