afni.nimh.nih.gov
| December 09, 2014 12:18PM | |
The next build of AFNI will include this feature -- it will be enabled from the popup menu attached to the top of the threshold slider -- the new 'Alpha' item.
If Alpha is turned on, then the opacity of the overlay ranges from 1 for above-threshold pixels down to the 'Floor' value -- set by the control just below 'Alpha' -- however, pixels with the threshold variable exactly equal to zero will not get the Floor value, but will get alpha=0.
In addition, the above-threshold pixel regions are outlined in black, unless the AFNI_EDGIZE_OVERLAY environment variable is set to NO -- this variable can be set interactively via the 'EditEnv' pseudo-plugin.
Note that the alpha (opacity) level at the pixel-wise level is scaled by the global opacity '1-9' control on the right side of the image viewer, so that '9' means that above-threshold pixels will be truly opaque, and '6' means they will be 6/9 opaque -- and lower opacity pixels will be have their opacity scaled down by the same factor.
Things will look better (less blocky) if you open 'Define Datamode' and set the resampling modes for the OLay and Stat to 'Li' (linear) rather than the default 'NN'.
An example image is linked to below, and hopefully shows up. Here, 'Alpha' is set to 'Linear', the 'Floor' is set to 0, the resampling modes are set to 'Li', and the effects of the black-outlining should be obvious.
If Alpha is turned on, then the opacity of the overlay ranges from 1 for above-threshold pixels down to the 'Floor' value -- set by the control just below 'Alpha' -- however, pixels with the threshold variable exactly equal to zero will not get the Floor value, but will get alpha=0.
In addition, the above-threshold pixel regions are outlined in black, unless the AFNI_EDGIZE_OVERLAY environment variable is set to NO -- this variable can be set interactively via the 'EditEnv' pseudo-plugin.
Note that the alpha (opacity) level at the pixel-wise level is scaled by the global opacity '1-9' control on the right side of the image viewer, so that '9' means that above-threshold pixels will be truly opaque, and '6' means they will be 6/9 opaque -- and lower opacity pixels will be have their opacity scaled down by the same factor.
Things will look better (less blocky) if you open 'Define Datamode' and set the resampling modes for the OLay and Stat to 'Li' (linear) rather than the default 'NN'.
An example image is linked to below, and hopefully shows up. Here, 'Alpha' is set to 'Linear', the 'Floor' is set to 0, the resampling modes are set to 'Li', and the effects of the black-outlining should be obvious.
