Description
What would you like to see added in this software?
While testing PETPrep I ran into this issue that will require some changes to spaces.py in niworkflows
(petprep) $ petprep /Users/martinnorgaard/Documents/GitHub/petprep/petprep/data/pet/ /Users/martinnorgaard/Documents/GitHub/petprep/petprep/data/pet/derivatives/petprep participant --no-msm --nprocs 4 --reference-frame 10 --seg wm --fs-subjects-dir /Users/martinnorgaard/Documents/GitHub/petprep/petprep/data/pet/derivatives/freesurfer/ --output-spaces petref
You are using PETPrep-25.0.0.dev337+gdffdb41.d20250610, and a newer version of PETPrep is available: 25.1.0.
Please check out our documentation about how and when to upgrade:
https://petprep.readthedocs.io/en/latest/faq.html#upgrading
Traceback (most recent call last):
File "/Users/martinnorgaard/anaconda3/envs/petprep/bin/petprep", line 8, in
sys.exit(main())
File "/Users/martinnorgaard/Dropbox/Mac/Documents/GitHub/petprep/petprep/cli/run.py", line 40, in main
parse_args()
File "/Users/martinnorgaard/Dropbox/Mac/Documents/GitHub/petprep/petprep/cli/parser.py", line 710, in parse_args
opts = parser.parse_args(args, namespace)
File "/Users/martinnorgaard/anaconda3/envs/petprep/lib/python3.10/argparse.py", line 1833, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/Users/martinnorgaard/anaconda3/envs/petprep/lib/python3.10/argparse.py", line 1866, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/Users/martinnorgaard/anaconda3/envs/petprep/lib/python3.10/argparse.py", line 2079, in _parse_known_args
start_index = consume_optional(start_index)
File "/Users/martinnorgaard/anaconda3/envs/petprep/lib/python3.10/argparse.py", line 2019, in consume_optional
take_action(action, args, option_string)
File "/Users/martinnorgaard/anaconda3/envs/petprep/lib/python3.10/argparse.py", line 1943, in take_action
action(self, namespace, argument_values, option_string)
File "/Users/martinnorgaard/Dropbox/Mac/Documents/GitHub/niworkflows/niworkflows/utils/spaces.py", line 723, in call
for sp in Reference.from_string(val):
File "/Users/martinnorgaard/Dropbox/Mac/Documents/GitHub/niworkflows/niworkflows/utils/spaces.py", line 356, in from_string
return [cls(_args[0], s) for s in allspecs]
File "/Users/martinnorgaard/Dropbox/Mac/Documents/GitHub/niworkflows/niworkflows/utils/spaces.py", line 356, in
return [cls(_args[0], s) for s in allspecs]
File "", line 43, in init
File "/Users/martinnorgaard/Dropbox/Mac/Documents/GitHub/niworkflows/niworkflows/utils/spaces.py", line 260, in _check_name
raise ValueError(
ValueError: space identifier "petref" is invalid.
Valid identifiers are: Fischer344, MNI152Lin, MNI152NLin2009aAsym, MNI152NLin2009aSym, MNI152NLin2009bAsym, MNI152NLin2009bSym, MNI152NLin2009cAsym, MNI152NLin2009cSym, MNI152NLin6Asym, MNI152NLin6Sym, MNI305, MNIColin27, MNIInfant, MNIPediatricAsym, MouseIn, NKI, NMT31Sym, OASIS30ANTs, PNC, RESILIENT, UNCInfant, VALiDATe29, WHS, dhcpAsym, dhcpSym, dhcpVol, fsLR, fsaverage, onavg, T1w, T2w, anat, fsnative, func, run, sbref, session, individual, dwi, asl
Do you have any interest in helping implement the feature?
Yes
Additional information / screenshots
No response