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AFNI and SUMA new features - May 2005 AFNI and SUMA new features - May 2005

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Submitted by rwcox. on 2005-05-02 14:11.

May 2005:

  • In the Scatterplot plugin, added overlay of the least squares fit line (in red) between the two sets of data being graphed.
  • The sub-brick choosers on the Define Overlay control panel will now resize themselves to fit longer sub-brick labels (as some people seem to generate via 3dDeconvolve). The old environment variable AFNI_BUCKET_LABELSIZE is now obsolete.
  • When writing NIfTI-1.1 '.nii' datasets, AFNI programs now include more AFNI header features in the .nii file, so that re-using such a file in another AFNI program is more likely to do what you expect.
  • When using waver -tstim, each stimulus time can now have a separate amplitude factor attached. Try, for example, this command:
      waver -dt 1.0 -GAM -peak 1.0 -tstim 3.2 17.9x2.0 23.1x-0.5 | 1dplot -stdin 
    Each time with an "x" after it is taken to have a scaling factor. For one possible use, see this page.
  • Modified 1dplot so that if the input (from a file or from stdin) is one long line of numbers, it will plot correctly. Before, you would have to transpose such a long line into a multi-line single-column file for graphing. This change makes it easier to use 1dplot -stdin with some programs such as nifti_tool.
  • The image window Button-3 popup menu now has an item to let you open the ROI drawing plugin directly.
  • 3dcalc now lets you specify that the (x,y,z) coordinates are in DICOM or SPM order.
    • The default remains that (x,y,z) correspond to the order that the dataset is stored on disk; you can see this order using the 3dinfo command.
    • If the new option -dicom or -RAI is given, then the coordinates to appear in DICOM standard (RAI) order, so that
      -x=Right  -y=Anterior   -z=Inferior
      +x=Left   +y=Posterior  +z=Superior
    • If the new option -SPM or -LPI is given, then the coordinates to appear in SPM (LPI) order, so that
      -x=Left   -y=Posterior  -z=Inferior
      +x=Right  +y=Anterior   +z=Superior
  • The AFNI graph window now draws little circles around graph points that correspond to time points are being 'ignored' by the grapher. The 'Ignore' level is set on the FIM->Ignore sub-menu, and is used to have the grapher not plot the first few time points of a dataset -- this is useful when graphing EPI time series, which might have the first few points be extra-bright.

3dMax Update

Posted by dglen at 2005-05-03 13:24
Updated 3dMax to calculate means of datasets. Also added -mask and -automask options for finding the min, max and/or mean over datasets.

3dMax and 3dhistog updates

Posted by dglen at 2005-05-19 18:03
3dMax now can count voxels (print the number of voxels included), and limits can be set for +/-/0 voxels with options -count, -positive, -negative, -zero, -non-positive -non-negative, non-zero.

3dhistog can take a minimum and maximum with the -min and -max options to force the range. This is similar to the Histogram plug-in. Useful for matching binning across datasets.

3dDWItoDT mask option

Posted by dglen at 2005-05-27 16:45
3dDWItoDT now allows a mask option to use any dataset as a mask for the computations. Previously, only an automask option was available.
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