could anyone tell me what is the difference between these two commands:
3dinfo striatum-structural-2mm | grep -i ‘template’
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!
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.
Thank you! So I guess this will tell the actual space and not just the header (in case of a mismatch between these two)?
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.
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