We are processing pcasl data with aslprep version 0.6.0 with pre-existing freesurfer outputs, and get the following error.
If I use –fs-no-reconall it works. Which are the main differences regarding the outputs? How can I solve the error and use pre-existing freesurfer outputs?
Thank you in advance,
Lucía
Command used (and if a helper script was used, a link to the helper script or the command generated):
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
ERROR: It appears that this subject ID is an existing
base/template from longitudinal processing (-base):
sub-209
If you are trying to re-run a -base template you
need to pass the -base and all -tp flags:
\' -base <templateid> -tp <tpNid> ... -all \'
(Instead of -all you can pass other flags, such
as -autorecon2 -autorecon3 to run only parts.)
Stderr:
Traceback:
RuntimeError: subprocess exited with code 1
Xcp_d is not designed to work with longitudinal freesurfer outputs. In general, BIDS apps expect to find freesurfer outputs in $SUBJECTS_DIR/$SUB. So, if you want to try using a longitudinal output, you would have to reorganize to match that convention. That is, move the set of freesurfer outputs you want to use into its own subjects dir, and rename it as sub-209 with no additional text.