Hi,

I installed pestica4 on a Mac (10.11) with Matlab 2015b and afni (Precompiled binary macosx_10.7_Intel_64: Jul 8 2016 (Version AFNI_16.2.01)). After some troubleshooting (due to some ugly OS X and Matlab interaction) pestica4 did run successfully after starting it with 
run_pestica.sh -d epiFile

Now I'd like to run 
slicemoco_newalgorithm.sh –d epiFile -r

The question now seems to be a basic one. It won't start but just gives back when starting within the folder where the epiFile (= OutBrick_run_025+orig.BRIK OutBrick_run_025+orig.HEAD) lives:

### output from shell:
slicemoco_newalgorithm.sh –d OutBrick_run_025+orig -r
Note that the physiologic fluctuation will not be regressed out (not recommended)
3D+time EPI dataset must be given
slicemoco_newalgorithm (distributed with PESTICA v4)
Algorithm: this script first runs slicewise in-plane (xy) 3DOF motion correction
then runs a slicewise 6DOF rigid-body correction for each slice
this script reads these motion parameters back in and regress on voxel timeseries
WARNING, make sure you have removed unsaturated images at start (such as first 4 vols)
You can test first volumes for spin saturation with: 3dToutcount | 1dplot -stdin -one
Is the first volume much higher than rest? If so, you may need to remove first several volumes first
If you don't know what this means, consult someone who does know, this is very important,
regression corrections (and analyses) perform poorly when the data has unsaturated volumes at the start
Simple method to remove 1st 4: 3dcalc -a "+orig[4..$]" -expr a -prefix .steadystate

Usage: slicemoco_newalgorithm.sh -d
-d = dataset: is the file prefix of
the 3D+time dataset to use and correct.
Note: this script will detect suffix for epi_filename
slicemoco_newalgorithm.sh -d -r
-r = perform in parallel with final PESTICA regression correction
this assumes PESTICA estimation steps 1-5 have been run and exist in subdir pestica4/
slicemoco_newalgorithm.sh -d -p
-p = same as -r option, but assuming you used PMU data instead of PESTICA for the correction
Recommended, run after running PESTICA or PMU correction, so we can incorporate all regressions in parallel:
slicemoco_newalgorithm.sh -d -r
OR, slicemoco_newalgorithm.sh -d -p
###

That is, slicemoco does not seem to recognize the epiFile. I did try including the absolute path which didn't change the output. Any idea?

An additional and unrelated question: Is it possible to explicitly feed in slice timing info in ms for each slice within the pestica4 pipeline, especially when using nifti files (because after converting DICOMs slice timing information gets lost)?

Thank you for your great tools!

Christian