Hi. I am afni_proc.pying data that has already been afni_proc.pyed. Here are the blocks for afni_proc.py #1:
despike tshift align tlrc volreg mask regress
. For afni_proc.py #2, I am trying to apply
blur mask regress
and, during the regression, apply a whole brain anat mask that I have already created. I was open the redundancy of recreating it with
, but afni_proc.py gave me an error during testing,
** ERROR: cannot apply anat mask
, despite the fact that I gave it
. Therefore, I am back to Square 1. I would like to use
-mask_import LABEL MSET
, but I do not know what LABEL is (subbrick label?), I do not know if I simultaneously still need to use -mask_apply and why I need to use/how I need to use the other regress or mask options listed in the -mask_import option in afni_proc.py -help.
LABEL is a name given to the mask for other operations (e.g., ROI regression), as well as being part of the resulting file name.
The -mask_import option previously required the LABEL to be from a fixed list of pre-defined masks (epi, anat, epi_anat, group, extents).
Yesterday I expanded that to allow for user-defined mask LABELs. So with that, you can apply an option pair such as:
-mask_import perfect_brain path/to/my/perfect_brain.nii.gz \
-mask_apply perfect brain \
Unfortunately, I forgot to push this commit before building new AFNI binaries last night, so I will start a new build for this soon. It should be ready by noon or 1, probably. Then you can see whether this is what you want.
Thanks for the suggestion,
Hi. I will test this soon. Thanks!
P.S.: To get a perfect brain, I would need to scan you!
Ha! This rasin’s hardly worth the sea of CSF it floats in…
Hi. Initial testing was successful. Thanks again.
Great, thanks for the update!