Usage Notes

Execution and the BIDS format

The fcdproc 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 fcdproc depends on the Installation method. The common parts of the command follow the BIDS-Apps definition. Example:

fcdproc --work_dir work/ --output_dir out/ --bids_dir  data/bids_root/

Further information about BIDS and BIDS-Apps can be found at the NiPreps portal.

Command-Line Arguments

fcdproc

Create fcd pipeline that can perform single subject processing, modeling and detecting of FCD lesion

fcdproc [OPTIONS]

Options

--version: Show the version and exit.

--work_dir <work_dir>: Required working directory

--analysis_mode <analysis_mode>

Options: preprocess | model | detect

--participant_label <participant_label>: subject id to be processed (the sub- prefix can be removed)

--controls <controls>: list of control subject with normal brains

--pt_positive <pt_positive>: list of patients with known fcd lesions

--pt_negative <pt_negative>: list of patients with MRI negative fcd lesions

--fs_reconall, --fs_no_reconall: option to run freesurfer reconstruction

--fs_subjects_dir <fs_subjects_dir>: path to existing subjects directory to reuse (default: OUTPUT_DIR/freesurfer)

--fs_license_file <fs_license_file>: path to Freesurfer licencse key file

--clean_workdir: Clears working directory of contents to save some space on user OS

--output_dir <output_dir>: Required output data directory

--bids_dir <bids_dir>: Required inputs BIDS data directory

The FreeSurfer license

fcdproc uses FreeSurfer tools, which require a license to run.

To obtain a FreeSurfer license, simply register for free at https://surfer.nmr.mgh.harvard.edu/registration.html.

When using manually-prepared environments or singularity, FreeSurfer will search for a license key file first using the $FS_LICENSE environment variable and then in the default path to the license key file ($FREESURFER_HOME/license.txt).

Using a previous run of FreeSurfer

Reconstructions for each participant will be checked for completeness, and any missing components will be recomputed. You can use the --f_subjects_dir flag to specify a different location to save FreeSurfer outputs. If precomputed results are found, they will be reused.

Support and communication. All bugs, concerns and enhancement requests for this software can be submitted here: https://github.com/InatiLab/fcdproc/issues.