Perfect! It is working! Thanks a lot,
Sophie. On Fri, 23 Sep 2011, Donna Dierker wrote: > 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 > --- 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
