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

[Andrew Wood]

Hi all,

Alex's images are really easy to make with the create_verify_image script
that we're running here at Biospective. We've added quite a number of
convenience functions (e.g. on-the-fly marching_cubes for surface overlays,
thresholding options for volume overlays, etc).

His PET to T1 image would be made with a call like this:
$ create_verify_image PET2T1_stx.png  \
-autocols 4 -width 2400 \
-row t1_stx.mnc color:gray surface_overylay:csf_stx.mnc:blue \
-row PET_stx.mnc color:gray surface_overylay:csf_stx.mnc:blue

Does anyone know where the ILT source code lives, and who is maintaining
it? It'd be great if we could feed these improvements back to the community.

Best,
Andrew

On Fri, Jan 23, 2015 at 2:24 PM, Paul GRAVEL <pgravel at bic.mni.mcgill.ca>
wrote:

> 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
>>
>>  _______________________________________________
> MINC-users at bic.mni.mcgill.ca
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>