Comments (3)
Also, by the way, I think it's more proper to call .as_posix()
rather than str
on Path
:
e.g. wd_layout = bids.BIDSLayout(str(Path(work_dir) / 'reportlets' / 'fitlins'))
from fitlins.
I'm also getting an odd error when I specify the workdir via -w
if I do -w /work-dir
it gets read in as /current_dir/ /work-dir
I don't think op.abspath
is working as it should.
Update, it seems to work if I use --workdir=<dir>
instead of -w <dir>
from fitlins.
Also: that function needs to create the dir if it does not exist (which it usually wont). Otherwise:
report_dicts = parse_directory(deriv_dir, opts.work_dir, analysis)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/fitlins/viz/reports.py", line 36, in parse_directory
wd_layout = bids.BIDSLayout(str(Path(work_dir) / 'reportlets' / 'fitlins'))
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/bids/grabbids/bids_layout.py", line 131, in __init__
**kwargs)
File "/opt/conda/envs/neuro/lib/python3.6/site-packages/grabbit/core.py", line 414, in __init__
raise ValueError("Search path {} doesn't exist.".format(p))
path.mkdir(parents=True, exist_ok=True)
from fitlins.
Related Issues (20)
- Premade BIDS Database Error HOT 3
- Fetch DataLad datasets HOT 2
- Update installation instructions
- Reports fail for models with only first-level analysis
- TypeError: slice indices must be integers or None or have an __index__ method
- --drop-missing still throws errors with missing regressors HOT 2
- Support for fsnative HOT 1
- Update test and example models to stats models 1.0
- Fitlins should point to https://bids-standard.github.io/stats-models/
- How to model BIDS dataset with no trial type? HOT 1
- Handle cases where a contrast is missing from the first level HOT 4
- ReadTheDocs isn't building HOT 5
- CI: Run nightly tests with pybids@master
- Add CLI command to generate reports HOT 4
- Regressor has extra item, causing mismatch HOT 8
- TypeError: unhashable type: 'list' in Loader HOT 6
- Contrasts missing from report HOT 1
- What does fitlins assume about slice time correction? HOT 2
- Fail gracefully if no files found HOT 1
- Fail gracefully if Contrast specification is incorrect
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from fitlins.