Problem with 3dTcat


I am encountering some problems when running 3dTcat on multiple subjects and I hope someone has an idea how to solve it :slight_smile:

I am using 3dTcat to concatenate multiple residual time courses extracted from SPM. They are in nifti format, such that I have a nifti-file for each volume (=1080 files). Here’s the command I’m using:

3dTcat -TR 2 -prefix 4D_res Res_*

I ran it for one participant first and it produced a BRIK and HEAD file that seem okay, but when I then run another participant the output BRIK file is much smaller than for the first participant (e.g. 674MB vs. 134 MB) though they are comparable with respect to the input files (same number and file sizes etc.). Weirdly, the header file says that the file size is 674MB, but the BRIK file is indeed much smaller and can also not be processed by 3dFWHMx later on.

I’m very new to AFNI and would greatly appreciate your help and ideas!

Many thanks in advance!


I think the syntax is a little bit off-- I don’t see a specific output name for the new file after prefix. I think your command should look something more like this:

3dTcat -tr 2 -prefix OUTPUTNAME   4D_res Res_*

That being said, I’m also not sure if there might not be other header issues from the file conversion.