[MINC-users] Outputting overlay of co-registered MINC files directly to a file

[Paul GRAVEL]

Thanks also Alex and Andrew!
Alex, very nice images!
I will look into using this tool more closely.
Best,
Paul


On Tue, 20 Jan 2015, Alex Zijdenbos wrote:

> Or you can use create_verify_image (bundled with ILT), and pretty simply
> create images like these:
>
> PET to T1 <https://dl.dropboxusercontent.com/u/5709165/MINC/PET2T1_stx.png>
> PET stx <https://dl.dropboxusercontent.com/u/5709165/MINC/PET_stx.png>
>
> -- A
>
>
> On Tue, Jan 20, 2015 at 6:44 PM, Andrew Janke <a.janke at gmail.com> wrote:
>
>> Claude and Vladimir's suggestions will certainly do what you are
>> requesting, but in case others are watching on, here is a somewhat
>> easier way to achieve what Claude posted albeit with slightly less
>> control on the chosen slice(s).
>>
>>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the cat"
>> input.mnc out.jpg
>>
>> If like me, you'd like a slice offset from the centre by 10% of the
>> volume size in the sagittal direction then do this:
>>
>>    mincpik -triplanar -tilesize 300 -horizontal -title "bob the cat"
>> -sagittal_offset_perc 10 input.mnc out.jpg
>>
>>
>> a
>>
>> On 21 January 2015 at 06:31, Claude LEPAGE <claude at bic.mni.mcgill.ca>
>> wrote:
>>> Hi Paul,
>>>
>>> Try something like this, in Perlish way:
>>>
>>>   `mincpik -clobber -slice 100 -axial -width 300 -lookup -spectral
>> $input /tmp/axial.jpg`;
>>>   `mincpik -clobber -slice 100 -coronal -width 300 -lookup -spectral
>> $input /tmp/coronal.jpg`;
>>>   `mincpik -clobber -slice 100 -sagittal -width 300 -lookup -spectral
>> $input /tmp/sagittal.jpg`;
>>>   `montage -tile 3x1 -background black -geometry 300x300+1+1
>> /tmp/axial.jpg /tmp/coronal.jpg /tmp/sagittal.jpg image_t1.jpg`;
>>>
>>> $input is you minc file in stx space. You can play with the
>>> colour scheme if you don't like spectral.
>>>
>>> I do the above in a script when I convert from DICOM/nii to minc
>>> in order to check the sanity of the minc files.
>>>
>>> Claude
>>> _______________________________________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>