I suspect you'll need to do more than that. There is the palette file "my_own_palette.palette" and the palette itself within that file. (A palette file can define several palettes.)
Because I don't know exactly which tags define what, I typically get a scene looking exactly how I want, with the palette file loaded and the right palette selected. Then I add a scene "Scene I'm happy with" and save the resulting scene file. Then I used a sed script to replace all the actual filenames with placeholders (e.g., Human.subject1.L.midthickness.coord becomes FIDUCIAL_FNAME). Then I use the template scene with a script to loop through subjects and swap variable names with actual filenames. On Sep 23, 2011, at 4:11 AM, Sophie Achard wrote: > > Dear Donna, > > Thanks for your answer. I did exactly what you mention. You are right, I > want to use the same palette for all the images. So I changed > into the scene file : > > <metricPaletteIndex> > <model><![CDATA[]]></model> > <overlay><![CDATA[-1]]></overlay> > <value><![CDATA[my_ownpalette]]></value> > </metricPaletteIndex> > > And I added the line in the spec file : > palette_file my_own_palette.palette > > The file my_own_palette.palette was generated using caret. > > But when I wanted to create the jpg files using the -show-scene command, > there was an output error saying : could not find 'my_ownpalette' > > In fact, when I am downloading the spec file using the GUI, I have to tick > the specific box specifying that I want to use my own palette file, it is > not ticked by default just as the .coord and .topo files. > > I think I am missing something to mention at the beginning to specify to > caret to get the correct palette file. > > Thanks, > > Best wishes, > > Sophie. > > On Thu, 22 Sep 2011, Donna Dierker wrote: > >> There probably is more than one way to do this. The way I'm used to >> batching images is using caret_command -show-scene with some TEMPLATE.scene >> file that has variable names like FIDUCIAL_FNAME for any files that vary. >> The palette file will probably remain constant across your subjects, so >> storing this in your scene and using that template scene is probably the way >> to go. >> >> For an example of how this works, see >> http://brainvis.wustl.edu/pub/caret/PALS_B12.LR.zip (login pub, password >> download) and see how preborder.sh interacts with TEMPLATE.check.*H.scene. >> (Scroll down to the check scenes near the end.) >> >> If this turns out to be far more complicated than what you have been doing, >> then tell me how you've been doing it. >> >> >> On Sep 22, 2011, at 3:16 AM, Sophie Achard wrote: >> >>> >>> Dear caret users, >>> >>> I've found a way to batch caret to be able to export color images using >>> specific template. My problem now is to specify to caret to use my own >>> palette. I know how to do this using the GUI, but when I want to batch it, >>> caret is not able to find my own palette. >>> >>> I've tried to add a line in the .spec file, to specify the new palette >>> file to use, but it seems caret could not read it by default. >>> >>> Thanks a lot for your help, >>> >>> Sophie. >>> _______________________________________________ >>> caret-users mailing list >>> [email protected] >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> >> >> _______________________________________________ >> caret-users mailing list >> [email protected] >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > > --- > Sophie Achard --- Research Fellow of the CNRS --- +33 476 57 43 52 > Grenoble Image Parole Signal Automatique, GIPSA-lab, INPG > Department : Images and Signal, > Team :Communication and Information in Complex Systems (CICS) > [email protected] > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
