[caret-users] spec print issue

Colin Reveley cmr25 at sussex.ac.uk
Fri Nov 2 14:08:10 CDT 2012


 a spec looks like this. they are all identical, except the actual data is
different in the files with those names. and the spec name is different.

the scene file is always the same. it's copied in as "THIS.scene" . i.e.
it's all a big template. I alter the individual scene files a little to
change thresholds.

I have a feeling that this template idea is my problem. I can't find
anything in the scene file xml to indicate whether or not to print scale
numbers. but it's a massive file and I don't really understand it obviously.

could this be to do with areacolor files? I make sure files with the right
names are there. there's no file missing error. but I find it confusing
that it always creates a new areacolor file when I start caret, rather than
use the one I put in the spec.
thanks..........

Colin

On 2 November 2012 18:52, Colin Reveley <cmr25 at sussex.ac.uk> wrote:

> does anyone know why my scene files print with the color bar, but not the
> numbers to go with it?
>
> I'm using caret_command -show-scene.
>
> the specs are very large and contain most kinds of data, including
> vector.gii. there are very many scenes in the scene file. the metric file
> has been collapsed by -metric-composite (or whatever) many times.
>
> the numbers show fine in the gui. it all works. just not print from
> command line. it also doesn't respect the amount that I've zoomed in on a
> surface, but that's a small thing.
>
> it would really be a help to get this working. there are very many specs
> and very many scenes and the plan was to script the scenes from each spec
> into a parameterized latex document section, then cat them all into a
> document. It all works except for this issue.
>
> the issue looks like this. I tried getting rid of all functional volume
> overlays and unchecking the display bar for volumes, but it still doesn't
> work. out of ideas.
>
> many thanks
>
> Colin
>
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BeginHeader
encoding ASCII
species Macaque
structure right
subject DB58
EndHeader
CLOSEDtopo_file ../CARET_SHARED/DB58.R.CLOSED.topo.gii
FIDUCIALcoord_file ../CARET_SHARED/DB58.R.MID.coord.gii
FIDUCIALcoord_file ../CARET_SHARED/DB58.R.MID2.coord.gii
FIDUCIALcoord_file ../CARET_SHARED/DB58.R.MID3.coord.gii
FIDUCIALcoord_file ../CARET_SHARED/DB58.R.MID4.coord.gii
FIDUCIALcoord_file ../CARET_SHARED/DB58.R.WM.coord.gii
FIDUCIALcoord_file ../CARET_SHARED/DB58.R.WM2.coord.gii
FIDUCIALcoord_file ../CARET_SHARED/DB58.R.WM3.coord.gii
FIDUCIALcoord_file ../CARET_SHARED/DB58.R.WM4.coord.gii
FIDUCIALcoord_file ../CARET_SHARED/DB58.R.PIAL.coord.gii
FIDUCIALcoord_file ../CARET_SHARED/DB58.R.PIAL2.coord.gii
FIDUCIALcoord_file ../CARET_SHARED/DB58.R.PIAL3.coord.gii
FIDUCIALcoord_file ../CARET_SHARED/DB58.R.PIAL4.coord.gii
FIDUCIALcoord_file ../CARET_SHARED/DB58.R.MWS.coord.gii
INFLATEDcoord_file ../CARET_SHARED/DB58.R.Inflated.coord.gii
INFLATEDcoord_file ../CARET_SHARED/DB58.R.Inflated2.coord.gii
INFLATEDcoord_file ../CARET_SHARED/DB58.R.Inflated3.coord.gii
INFLATEDcoord_file ../CARET_SHARED/DB58.R.Inflated4.coord.gii
VERY_INFLATEDcoord_file ../CARET_SHARED/DB58.R.VeryInflated.coord.gii
VERY_INFLATEDcoord_file ../CARET_SHARED/DB58.R.VeryInflated2.coord.gii
VERY_INFLATEDcoord_file ../CARET_SHARED/DB58.R.VeryInflated3.coord.gii
VERY_INFLATEDcoord_file ../CARET_SHARED/DB58.R.VeryInflated4.coord.gii
volume_anatomy_file  ../CARET_SHARED/MTR.nii.gz
volume_anatomy_file  ../CARET_SHARED/FA.nii.gz
volume_anatomy_file  ../CARET_SHARED/MTR_500.nii.gz
volume_anatomy_file  ../CARET_SHARED/FA_500.nii.gz
volume_anatomy_file  ../CARET_SHARED/MTR_1000.nii.gz
volume_anatomy_file  ../CARET_SHARED/FA_1000.nii.gz
volume_anatomy_file  f1.nii.gz
volume_functional_file  ../CARET_SHARED/MTR_GM.nii.gz
volume_functional_file  ../CARET_SHARED/FA_GM.nii.gz
volume_functional_file  ../CARET_SHARED/WL_GM.nii.gz
volume_functional_file  ../CARET_SHARED/WP_GM.nii.gz
volume_functional_file  ../CARET_SHARED/WS_GM.nii.gz
volume_functional_file  ../CARET_SHARED/FA.nii.gz
volume_functional_file  ../CARET_SHARED/MTR_500.nii.gz
volume_functional_file  ../CARET_SHARED/FA_500.nii.gz
volume_functional_file  ../CARET_SHARED/MTR_1000.nii.gz
volume_functional_file  ../CARET_SHARED/FA_1000.nii.gz
volume_segmentation_file ../CARET_SHARED/R.PIALSEG_250.nii.gz
volume_segmentation_file ../CARET_SHARED/R.WMSEG_250.nii.gz
volume_segmentation_file ../CARET_SHARED/R.MIDSEG_250.nii.gz
volume_segmentation_file ../CARET_SHARED/R.CASE5_SEG.nii.gz
volume_segmentation_file ../CARET_SHARED/CC_TRACKS_BOTH_SEG.nii.gz
volume_functional_file f1.nii.gz
volume_functional_file f2.nii.gz
volume_functional_file f3.nii.gz
volume_functional_file d1.nii.gz
volume_functional_file d2.nii.gz
volume_functional_file d3.nii.gz
volume_functional_file disp1_inverse.nii.gz
volume_functional_file disp2_inverse.nii.gz
volume_functional_file disp3_inverse.nii.gz
volume_functional_file CC_TR_ALL.nii.gz
volume_functional_file CASE5_TR.nii.gz
volume_functional_file CC_TR_ALL_ln.nii.gz
volume_functional_file CASE5_TR_ln.nii.gz
scene_file R.THIS.scene
metric_file R.THIS.metric
surface_shape_file R.THIS.surface_shape
paint_file R.THIS.paint
area_color_file R.THIS.areacolor
border_color_file R.THIS.bordercolor
borderproj_file R.THIS.borderproj
volume_functional_file CASE5_TR_GM.nii.gz
volume_functional_file CC_TR_ALL_GM.nii.gz
volume_functional_file CASE5_TR_ln_GM.nii.gz
volume_functional_file CC_TR_ALL_ln_GM.nii.gz
vector_file dyads1_d1_inverse.LR.vector.gii
vector_file dyads1_f1.LR.vector.gii
vector_file dyads2_d2_inverse.LR.vector.gii
vector_file dyads2_f2.LR.vector.gii
vector_file dyads3_d3_inverse.LR.vector.gii
vector_file dyads3_f3.LR.vector.gii


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