Hi All,
I am using FSL v3.3 on unix/sun solaris although I did use v4.0.2, too, with the same results.
I am trying to use slicer to create a "lightbox" view as a gif file.
The input volume dimensions are [ 90 x 86 x 40 ] (after using avwroi++/fslroi).
The commands I use are:
% slicer inVol -lut greyscale -s 1.25 -u -i 0 742470 -A 4500 inVol.ppm
% convert -colors 100 inVol.ppm gif:inVol.gif
I expected the output ppm/gif files to have these dimensions:
x: 90 * 40 * 1.25 = 4500 (ie, xdim * numSlices * slicerScale)
y: 86 * 1.25 = 107.5 (ydim * slicerScale)
(Not sure what to do with fractional voxels -- floor or ceil?)
But the resulting ppm/gif files do not have the dimensions I expected:
% montage -verbose inVol.ppm /dev/null
inVol.ppm PNM 4407x216+0+0 PseudoClass 256c 8-bit 929.6kb 0.080u 0:01
% montage -verbose inVol.gif /dev/null
inVol.gif GIF 4407x216+0+0 PseudoClass 128c 8-bit 255.1kb 0.120u 0:01
Can anyone help me with my confusion?
Also, in light of a previous question about using slicer to get a sagittal view, I see the -x/y/z
<slice> switch. Do I need to specify each slice I want:
slicer inVol ... -x -1 -2 -3 ... inVol.ppm
or
slicer inVol ... -x -1 -x -2 -x -3 ... inVol.ppm
Is there an equivalent to the -A switch but for the other orientations (sagittal and coronal)?
Thanks for any help,
- BettyAnn
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