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

Fri Jan 23 15:27:00 EST 2015

ok, it is here: https://github.com/BIC-MNI/ILT

On Fri, Jan 23, 2015 at 3:22 PM, Andrew Janke <a.janke at gmail.com> wrote:

> it's on packages in the tgz directory.
>
> a
> On 24/01/2015 5:57 AM, "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
> >
> _______________________________________________
> 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