difference between 2 commands

AFNI Message Board
1

Hi

could anyone tell me what is the difference between these two commands:

3dinfo striatum-structural-2mm | grep -i ‘template’

and

3dinfo -prefix -av_space striatum-structural-2mm

I found them both as suggestion to check the space of a file / image but I am getting different answers from both!

2

The “av_space” gives the AFNI view equivalent, even for NIFTI datasets, so the options are +orig, +acpc, +tlrc. It doesn’t really tell you what space the dataset is in. You may want “3dinfo -space” instead.

3

Thank you! So I guess this will tell the actual space and not just the header (in case of a mismatch between these two)?

4

I would think you want “3dinfo -space” only as the most convenient way to find the template space of a dataset, and you probably don’t need the other methods. Note, the space is assumed from either an AFNI format attribute that is attached to the dataset during alignment to a template or from sform_code r qform_code in a NIFTI dataset. These can be wrong for a variety of reasons, so you should know what operations have been performed on the datasets to be sure they are in the right template space.

5

Thank you! That makes sense.

So that means both my datasets should be in MNI though the header says one is in TLRC
Because I normalised that one to a MNI mask at the end of my preprocessing pipeline.
But one may be the “FSL Flavour” as I downloaded it from FSL, I guess