[MINC-users] NIfTI to MINC revisited

[Vladimir S. FONOV]

Hello Simon,

can you try itk_convert from minc-toolkit to perform conversion? (
/ipl/quarantine/experimental/mt/bin/itk_convert , source
/ipl/quarantine/experimental/mt/minc-toolkit-config.sh first)

On Tue, Aug 14, 2012 at 8:33 AM, Simon Eskildsen <eskild at gmail.com> wrote:
> 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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-- 
Best regards,

 Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com