[MINC-users] NIfTI to MINC revisited

[Simon Eskildsen]

Hi Andrew,

On Tue, Aug 14, 2012 at 2:16 PM, Andrew Janke <a.janke at gmail.com> wrote:
> I'll stand by my "sufficient" stance!  I am guessing that these .nii
> images come from FSL (by the complete sform and qform
> transformations).

They have been converted from dicom using SPM, no fiddling (according
to my colleague).

> If so then what you would really need to write is a
> fsl2mnc and mnc2fsl where the output of fsl2mnc would be a minc file
> and a .xfm. The xfm would represent the transformation from native to
> standard space from the FSL nii file (the qform transformation).

Sounds like a fun project for the weekend.

> The conversion of a fsl .nii file to a minc will (from memory)
> concatenate these two transformations into one and when you then
> convert back to nii this will only be seen as an sform transformation.
> This will manifest itself in what you are seeing.

Makes sense.

> So you have two options.
>
> 1) write fsl2mnc!

Weekend project.

> 2) If you are just doing minc processing (no fiddling with
> registration/co-ordinates) then I'd convert back to a .nii .img+.hdr
> pair and replace the new header with the original.

This was my original plan. However, it turned out that importing minc1
(no support for minc2) files directly into SPM solved the issue. Maybe
my weekend is saved.

Simon

>
>
> a
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