gdevenyi
commented
7 years ago Usage: ConvertScalarImageToRGB imageDimension inputImage outputImage mask colormap [customColormapFile] [minimumInput] [maximumInput] [minimumRGBOutput=0] [maximumRGBOutput=255] <vtkLookupTable>
Possible colormaps: grey, red, green, blue, copper, jet, hsv, spring, summer, autumn, winter, hot, cool, overunder, custom
> ConvertScalarImageToRGB 3 /opt/quarantine/resources/nifti/mni_icbm152_nlin_sym_09c/mni_icbm152_t1_tal_nlin_sym_09c_mask.nii /tmp/rgb.nii.gz none redInvestigate custom map format to do nice distinct labels.
and
COMMAND:
CreateTiledMosaic
Render a 3-D image volume with optional Rgb overlay.
OPTIONS:
-i, --input-image inputImageFilename
Main input is a 3-D grayscale image.
-r, --rgb-image rgbImageFilename
An optional Rgb image can be added as an overlay. It must have the same image
geometry as the input grayscale image.
-x, --mask-image maskImageFilename
Specifies the ROI of the RGB voxels used.
-a, --alpha value
If an Rgb image is provided, render the overlay using the specified alpha
parameter.
-e, --functional-overlay [rgbImageFileName,maskImageFileName,<alpha=1>]
A functional overlay can be specified using both and rgb image and a mask
specifying where that rgb image should be applied. Both images must have the
same image geometry as the input image. Optionally, an alpha parameter can be
specified.Note that more than one functional overlays can be rendered, the order
in which they are specified on the command line matters, and rgb images are
assumed to be unsigned char [0,255].
-o, --output tiledMosaicImage
The output is the tiled mosaic image. Without an RGB overlaywe do not alter the
intensity values of the input image. Therefore, the output suffix needs to be
associated with a format that supports float images (not .jpg or .png). If one
or more RGB overlays are supported then we rescale the input image intensities
to also be in the range of [0,255] which permits a .png or .jpg output.
-t, --tile-geometry RxC
The tile geometry specifies the number of rows and columns in the output image.
For example, if the user specifies '5x10', then 5 rows by 10 columns of slices
are rendered. If R < 0 and C > 0 (or vice versa), the negative value is selected
based on direction.
-d, --direction 0/1/2/x/y/(z)
Specifies the direction of the slices. This can be based on the how the image is
stored in memory or can be based on how the image is aligned in physical space.
If no direction is specified, the z-direction (axial?) is chosen.
-p, --pad-or-crop padVoxelWidth
[padVoxelWidth,<constantValue=0>]
[lowerPadding[0]xlowerPadding[1],upperPadding[0]xupperPadding[1],constantValue]
The user can specify whether to pad or crop a specified voxel-width boundary of
each individual slice. For this program, cropping is simply padding with
negative voxel-widths. If one pads (+), the user can also specify a constant pad
value (default = 0). If a mask is specified, the user can use the mask to define
the region, by using the keyword "mask" plus an offset, e.g. "-p mask+3".
-s, --slices Slice1xSlice2xSlice3...
numberOfSlicesToIncrement
[numberOfSlicesToIncrement,<minSlice=0>,<maxSlice=lastSlice>]
This option gives the user more control over what slices to use for rendering.
The user can specify specific slices for a particular order. Alternatively the
user can specify the number slices to increment with the optional specification
of which slices to start and end the sequence. A negative value for the
numberOfSlicesToIncrement causes rendering in the reverse order. For the third
option, minSlice < maxSlice. If a mask is specified, the user can use the mask
to define the region, by using the keyword "mask" plus an offset, e.g. "-s
[1,mask-3,200]".For the third option, minSlice < maxSlice.
-f, --flip-slice flipXxflipY
Flip individual slice images horizontally and/or vertically, specified e.g. as
'0x1' or '1x1'.
-g, --permute-axes doPermute
Permute (or swap) the axes of the individual slice images.
-h
Print the help menu (short version).
--help
Print the help menu. #Example
> CreateTiledMosaic -i /opt/quarantine/resources/nifti/mni_icbm152_nlin_sym_09c/mni_icbm152_t1_tal_nlin_sym_09c.nii -r /tmp/rgb.nii.gz -a 0.4 -o test.png -f 0x1
How?