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

[Vladimir S. FONOV]

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