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

[Alex Zijdenbos]

I'd say so. It's been available forever - I actually always assumed it was
on github :)

For those who are wondering, ILT stands for Image Layout Toolkit. It was
written by David MacDonald as a generic perl library for creating
verification images. create_verify_image is the main script that lets you
generate images of the kind I sent along; typically, you define
cross-sections through a volume horizontally, and add rows of images with
overlays and etc vertically.

-- A

On Fri, Jan 23, 2015 at 2:56 PM, Vladimir S. FONOV <vladimir.fonov at gmail.com
> wrote:

> Ok, I see it on cvs.bic.mni.mcgill.ca
> Does it mean that i can transfer it to the github ?
>
> On Fri, Jan 23, 2015 at 2:53 PM, Alex Zijdenbos <zijdenbos at gmail.com>
> wrote:
>
> > Hi Vladimir,
> >
> > Definitely not - ILT should be part of MINC and friends. It's used by
> > CIVET, but that's about it, much like CIVET uses mincmath.
> >
> > -- A
> >
> > On Fri, Jan 23, 2015 at 2:49 PM, Vladimir S. FONOV <
> > vladimir.fonov at gmail.com
> > > wrote:
> >
> > > Isn't it all part of CIVET?  Then Claude will be the one maintaining
> it.
> > >
> > >
> > > On Fri, Jan 23, 2015 at 2:46 PM, Andrew Wood <andrew at biospective.com>
> > > wrote:
> > >
> > > > 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
> > > > > 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
> > > >
> > >
> > >
> > >
> > > --
> > > Best regards,
> > >
> > >  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
> > > _______________________________________________
> > > 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
> >
>
>
>
> --
> Best regards,
>
>  Vladimir S. Fonov ~ vladimir <dot> fonov <at> gmail <dot> com
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
>