PowerPoint Presentation - Activation Delays in FMRI: Estimation and Variability

7/2/2004 SSCC/NIMH 55

Colorizing results with ScaleToMap:

•This step is no longer necessary with SUMA’s new interface for colorizing data.

•In the old days, ScaleToMap was the only way for getting node-based results into SUMA

•Execute: source run_ScaleToMap

•ScaleToMap     -input   out_Del.1D.dset 0 6         \
              -cmap    afni_p20                \
                  -apr     30                      \
               -msk     -3.0 -0.1               \
               -nomsk_col                       \
               > out_Del.1D.col

H-input : Specify the 1D format input file and the columns containing the node index and the node data

H-cmap : Specify the colormap to use.

ÂHere we are using AFNI’s standard colormaps (positive, 20 colors).

ÂCould use your own colormaps, see MakeColorMap

H-apr: AFNI positive range value.

ÂScaling a la AFNI, other scaling methods that do not require 0 à range or –range àrange are also available

ÂWhen data are integer valued (such as ROI datasets), you can use a direct mapping where a node with value i gets mapped to the ith color in the map.

H -msk: Mask data values in the specified range (inclusive)

H-nomsk_col: Do not color masked nodes (default is a dark gray).

ÂYou can specify your own mask color

HThe output of ScaleToMap is to stdout, which can be redirected with ‘ > ‘ symbol to a text file