Usage¶
Warning
As of FMRIPREP 1.0.12, the software includes a tracking system
to report usage statistics and errors. Users can opt-out using
the --notrack
command line argument.
Execution and the BIDS format¶
The fmriprep
workflow takes as principal input the path of the dataset
that is to be processed.
The input dataset is required to be in valid BIDS format, and it must include at least one T1w structural image and
(unless disabled with a flag) a BOLD series.
We highly recommend that you validate your dataset with the free, online
BIDS Validator.
The exact command to run fmriprep
depends on the Installation method.
The common parts of the command follow the BIDS-Apps definition.
Example:
fmriprep data/bids_root/ out/ participant -w work/
Command-Line Arguments¶
The docker wrapper CLI¶
The fMRIPrep on Docker wrapper
This is a lightweight Python wrapper to run fMRIPrep. Docker must be installed and running. This can be checked running
docker info
Please report any feedback to our GitHub repository (https://github.com/poldracklab/fmriprep) and do not forget to credit all the authors of software that fMRIPrep uses (https://fmriprep.readthedocs.io/en/latest/citing.html).
usage: fmriprep-docker [-h] [--version] [-i IMG] [-w WORK_DIR]
[--output-grid-reference OUTPUT_GRID_REFERENCE]
[--template-resampling-grid TEMPLATE_RESAMPLING_GRID]
[--fs-license-file PATH] [--use-plugin PATH] [-f PATH]
[-n PATH] [-p PATH] [--shell] [--config PATH]
[-e ENV_VAR value] [-u USER]
[bids_dir] [output_dir] [{participant}]
Positional Arguments¶
bids_dir | |
output_dir | |
analysis_level | Possible choices: participant |
Named Arguments¶
-h, --help | show this help message and exit |
--version | show program’s version number and exit |
-i, --image | image name |
Wrapper options¶
Standard options that require mapping files into the container
-w, --work-dir | path where intermediate results should be stored |
--output-grid-reference | |
Deprecated after FMRIPREP 1.0.8. Please use –template-resampling-grid instead. | |
--template-resampling-grid | |
Keyword (“native”, “1mm”, or “2mm”) or path to an existing file. Allows to define a reference grid for the resampling of BOLD images in template space. Keyword “native” will use the original BOLD grid as reference. Keywords “1mm” and “2mm” will use the corresponding isotropic template resolutions. If a path is given, the grid of that image will be used. It determines the field of view and resolution of the output images, but is not used in normalization. | |
--fs-license-file | |
Path to FreeSurfer license key file. Get it (for free) by registering at https://surfer.nmr.mgh.harvard.edu/registration.html | |
--use-plugin | nipype plugin configuration file |
Developer options¶
Tools for testing and debugging FMRIPREP
-f, --patch-fmriprep | |
working fmriprep repository | |
-n, --patch-niworkflows | |
working niworkflows repository | |
-p, --patch-nipype | |
working nipype repository | |
--shell | open shell in image instead of running FMRIPREP |
--config | Use custom nipype.cfg file |
-e, --env | Set custom environment variable within container |
-u, --user | Run container as a given user/uid |
Debugging¶
Logs and crashfiles are outputted into the
<output dir>/fmriprep/sub-<participant_label>/log
directory.
Information on how to customize and understand these files can be found on the
nipype debugging
page.
Support and communication¶
The documentation of this project is found here: http://fmriprep.readthedocs.org/en/latest/.
All bugs, concerns and enhancement requests for this software can be submitted here: https://github.com/poldracklab/fmriprep/issues.
If you have a problem or would like to ask a question about how to use fmriprep
,
please submit a question to NeuroStars.org with an fmriprep
tag.
NeuroStars.org is a platform similar to StackOverflow but dedicated to neuroinformatics.
All previous fmriprep
questions are available here:
http://neurostars.org/tags/fmriprep/
To participate in the fmriprep
development-related discussions please use the
following mailing list: http://mail.python.org/mailman/listinfo/neuroimaging
Please add [fmriprep] to the subject line when posting on the mailing list.
Not running on a local machine? - Data transfer¶
If you intend to run fmriprep
on a remote system, you will need to
make your data available within that system first.
For instance, here at the Poldrack Lab we use Stanford’s HPC system, called Sherlock. Sherlock enables the following data transfer options.
Alternatively, more comprehensive solutions such as Datalad will handle data transfers with the appropriate settings and commands. Datalad also performs version control over your data.