I have installed pestica4 on a mac (10.11.6) with matlab 2016a and
AFNI Precompiled binary macosx_10.6_Intel_64: Jan 1 2016 (Version AFNI_16.0.00).

I have several multiband runs, all MB factor 3 and 72 slices, which I would like to process
with pestica and slomoco. I have removed the first 4 volumes and insured that the TR (2.3 sec)
is still specified in the header of these *.nii.gz files acquired on a Siemens Skyra with Siemens'
multiband WIP.
I have revised setup_pestica.sh to point to my pestica installation. I insured that the pestica4
directory with subdirectories was in my matlab path and the main pestica4 directory is in
my shell's path.
I ran genSMStimeshiftfile(3, 72, 2.3) which generated a row of values. Most 1D files are a column
of values, so I tried to3d with both a row of values (separated by spaces), and I tried it again
with a column of values:
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> to3d -epan -time:zt 72 124 2300 @tshiftfile_ms.1D -prefix test run3_pilot001_124tr.nii.gz
++ to3d: AFNI version=AFNI_16.0.00 (Jan 1 2016) [64-bit]
++ Authored by: RW Cox
++ It is best to use to3d via the Dimon program.
*+ WARNING: TR expressed in milliseconds will be converted to TR=2.300000s
++ Counting images: *+ WARNING: If you are performing spatial transformations on an oblique dset,
such as run3_pilot001_124tr.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:run3_pilot001_124tr.nii.gz is 2.289013 degrees from plumb.
total=8928 2D slices
++ Oblique dataset:run3_pilot001_124tr.nii.gz is 2.289013 degrees from plumb.
++ Each 2D slice is 128 X 128 pixels
++ Image data type = short
++ Reading images: ..........................................
*+ WARNING: *** ILLEGAL INPUTS (cannot save) ***
Axes orientations are not consistent!
++ Making widgetsError: attempt to add non-widget child "dsm" to parent "to3d" which supports only widgets
=================================
As you can see afni is unhappy with the orientation of the axes and cannot save. I don't understand its difficulties or how to fix them. Afni can clearly get info about the image and display the image. Do you have any advice? Thank you for your help.
=================================
>3dinfo run3_pilot001_124tr.nii.gz
++ 3dinfo: AFNI version=AFNI_16.0.00 (Jan 1 2016) [64-bit]
Dataset File: run3_pilot001_124tr.nii.gz
Identifier Code: AFN_klivakcqOOBw0QDOoyXU3w Creation Date: Sat Apr 15 18:46:52 2017
Template Space: ORIG
Dataset Type: Echo Planar (-epan)
Byte Order: LSB_FIRST {assumed} [this CPU native = LSB_FIRST]
Storage Mode: NIFTI
Storage Space: 292,552,704 (293 million [mega]) bytes
Geometry String: "MATRIX(1.998404,0.052876,-0.059869,-131.6299,0.052727,-1.999297,-0.005782,132.101,0.060004,-0.004199,1.998994,-24.68394):128,128,72"
Data Axes Tilt: Oblique (2.289 deg. from plumb)
Data Axes Approximate Orientation:
first (x) = Right-to-Left
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient RPI]
R-to-L extent: -131.630 [R] -to- 122.370 [L] -step- 2.000 mm [128 voxels]
A-to-P extent: -121.899 [A] -to- 132.101 [P] -step- 2.000 mm [128 voxels]
I-to-S extent: -24.684 -to- 117.309 [S] -step- 2.000 mm [ 72 voxels]
Number of time steps = 124 Time step = 2.30000s Origin = 0.00000s
-- At sub-brick #0 'run3_pilot001.ni[4]' datum type is short: 0 to 1767
-- At sub-brick #1 'run3_pilot001.ni[5]' datum type is short: 0 to 1364
-- At sub-brick #2 'run3_pilot001.ni[6]' datum type is short: 0 to 1372
** For info on all 124 sub-bricks, use '3dinfo -verb' **
----- HISTORY -----
[dpat@feckless.convert.slhs.arizona.edu: Sat Apr 15 18:46:52 2017] 3dTcat -verb -prefix PreprocDetails/run3_pilot001_124tr.nii.gz 'run3_pilot001.nii.gz[4..$]'