Howdy -

Question 1: 3dcalc doesn't seem to care that .afnirc contains the line:

AFNI_ORIENT = lpi

Should it? Moreover, even though 3dinfo reports the dataset that I'm using with 3dcalc has -orient LPI, the processing seems to be occurring using RAI coords.

Question 2: this code produces a mask where x values [-8, infinity) are set to 1, and others are 0:

3dcalc -LPI -a abscon__mni_brain_mni.nii.gz -prefix test -expr 'ispositive(x+10)'

Assuming that 0 doesn't count as positive (so that x=-10 does not evaluate to true) then it appears that values of (-10, infinity) should be set to 1. Since my underlay has 1mm resolution, it won't let me move to non-integral values, so if that's right, (-9, infinity) should be set to 1; in other words, the current results seem off by one.

Am I missing something? Or could it be due perhaps to my voxels being 2.5mm, so that without resampling to 1mm the results are off by a sub-voxel increment? Here's the first bit from 3dinfo on the dataset:

Dataset File:    test+tlrc
Identifier Code: XYZ_igvjBM0klQrJ5o5KQc4MLg  Creation Date: Tue Aug 26 18:20:24 2014
Template Space:  MNI
Dataset Type:    Echo Planar (-epan)
Byte Order:      LSB_FIRST [this CPU native = LSB_FIRST]
Storage Mode:    BRIK
Storage Space:   3,708,984 (3.7 million [mega]) bytes
Geometry String: "MATRIX(-2.5,0,0,90,0,-2.5,0,125.5,0,0,2.5,-72):73,87,73"
Data Axes Tilt:  Plumb
Data Axes Orientation:
  first  (x) = Left-to-Right
  second (y) = Posterior-to-Anterior
  third  (z) = Inferior-to-Superior   [-orient LPI]
R-to-L extent:   -90.000 [R] -to-    90.000 [L] -step-     2.500 mm [ 73 voxels]
A-to-P extent:   -89.500 [A] -to-   125.500 [P] -step-     2.500 mm [ 87 voxels]
I-to-S extent:   -72.000  -to-   108.000 [S] -step-     2.500 mm [ 73 voxels]
Number of values stored at each pixel = 2
  -- At sub-brick #0 'setA_mean' datum type is float:            0 to             1
  -- At sub-brick #1 'setA_Tstat' datum type is float:            0 to             1