How to specify interleaved slices in 3dTcat

AFNI Message Board
1

Hi
I have several .nii files for a single object and I’m trying to put them in a single file. When I use
3dTcat -tr 3.0 -prefix output+orig *.nii
everything works fine and the program generates 2 files for me. But I have two questions:

1: My slices are interleaved, how can I specify it in 3dTcat? I know that I should use something like this " fred+orig[0…$(2),1…$(2)] " but I don’t know where to put this sentence.

2: Is there anyway of generating a single .nii.gz file instead of a BRIK and a HEAD file?

2

  1. I guess this was from the other thread “-tpattern alt+z”.

  2. Try “-prefix output.nii.gz”.

  • rick