tamsinrogers
commented
2 months ago Hi @suxpert, thanks for reaching out.
In terms of the command you are running, it will depend on what’s in your $BIDS/derivatives/fmriprep. The issue here is likely that C-PAC is expecting something from fmriprep that isn’t included in your fmriprep outputs.
Specifically, the timeseries for the ingress pipeline is not being pulled in.
Resources:
['pipeline-ingress_desc-confounds_timeseries']For some first steps, I can direct you to some documentation specific to pulling regressors from the fMRIPrep Output directory. The derivatives C-PAC should run with this config are listed here .
In your case, it looks like the fmriprep outputs either don’t have regressors or the regressors aren’t named how C-PAC expects them to be. Depending on what you have and what you want, you should be able to run with a custom pipeline config like one of these:
(Create regressors instead of ingressing them, don’t write them out):
FROM: fmriprep-ingress
nuisance_corrections:
2-nuisance_regression:
ingress_regressors:
run: Off(Create regressors instead of ingressing them, do write them out):
FROM: fmriprep-ingress
nuisance_corrections:
2-nuisance_regression:
ingress_regressors:
run: Off
create_regressors: On_(Replace global_signal, white_matter with the column names in their fmriprep output *_desc-confounds_timeseries.tsvfile)_:
FROM: fmriprep-ingress
nuisance_corrections:
2-nuisance_regression:
run: [Off]_(Use different regressors from frmiprep than global_signal, white_matter)_:
FROM: fmriprep-ingress
nuisance_corrections:
2-nuisance_regression:
ingress_regressors:
Regressors:
Columns: [global_signal, white_matter]Looking at your C-PAC-generated data config, this looks to be causing an issue - you will need a data config (until this in progress feature is completed). Looking at the issue you linked to, here is the documentation on how to format the config with fmriprep ingress. The data config should look similar to this for one subject:
-site: site-1
subject_id: 01
unique_id: 02
derivatives_dir: /bids_dir/derivatives/fmriprep/sub-01/ses-01I'd also recommend taking a look at a recently developed C-PAC feature that allows for the ability to ingress FMRIPrep output data directly into the C-PAC resource pool. This feature allows users to perform further processing on that data. There is some additional explanation regarding the ingress process and fMRIPrep regressors in this PR, and a similar issue that may be good to have as a reference point was resolved here.
Could you clarify exactly what kind of additional post-processing you are looking for C-PAC to do in this instance? Any additional information you can provide will help us point you in the right direction here as we continue to compile answers to your questions in Acceptance Criteria.
suxpert
Describe the bug
C-PAC seems too complex (for me) to correctly config, and after going through the not-well-written document, I still have no idea how could I run C-PAC on top of derivated data from fmriprep. Since the docker image print almost all its pipeline/config options as optional, I tried calling it as a BIDS-app with only nessesary arguments (see command below). Then C-PAC crashed saying C-PAC failed to start, see log for details.
I've checked for #2085, which show the same error as I met, but from #2085, I still do not know how to makes C-PAC run correctly.
To reproduce
docker pull fcpindi/c-pacdocker pull nipreps/fmriprepdocker run .... nipreps/fmriprep --fs-no-reconall $BIDS $BIDS/derivatives/fprep participantdocker run .... fcpindi/c-pac -preconfig fmriprep-ingress $BIDS/derivatives/fprep $BIDS/derivatives/cpac test_configPreconfig
Custom pipeline configuration
No response
Run command
Expected behavior
This command specified nothing but a pre-configured pipeline
fmriprep-ingress, since the output of fmriprep is clear enough for any post-processing tools to understand, I would expect any BIDS-apps that said to be compatible with fmriprep be good to run without any issue.Acceptance criteria
data_config.yml, is the given sample everything we need in the file, or should I include such a snippet in some data_config file that have been generated viautils data-config? It seems those config files differs a lot!C-PAChave--participant-labeletc to filtering the BIDS, and for BIDS-apps likefmriprep,XCP-D, they all accept the--bids-filter-filefor filtering, why doC-PACuse a different syntax?Screenshots
logs and generated config files:
C-PAC version
v1.8.7
Container platform
Docker
Docker and/or Singularity version(s)
Docker version 26.1.5-ce
Additional context
No response