Overview
This pipleine runs pre-processing, group level decomposition, quality control and dual regression on data ready for processing. It is fully customisable by the configuration file or can be run using command line arguments.
Please see NFACT Pre-Processing, NFACT Decomposition, NFACT Quality Control and NFACT Dual Regression for further details
Usage
nfact [-h] [-l LIST_OF_SUBJECTS] [-s SEED [SEED ...]] [-o OUTDIR]
[-n FOLDER_NAME] [-c CONFIG] [-P] [-Q] [-D] [-O] [-w WARPS [WARPS ...]]
[-b BPX_PATH] [-r ROI [ROI ...]] [-f FILE_TREE] [-sr SEEDREF] [-t TARGET2]
[-d DIM] [-a ALGO] [-rf ROI] [--threshold THRESHOLD]
- General Options:
- -h, --help
Shows help message and exit
- Pipeline inputs:
- -l, --list_of_subjects
Absolute filepath to a text file containing absolute path to subjects. Consider using nfact_config to create subject list.
- -s, --seed
Relative path to either a single or multiple seeds. If multiple seeds given then include a space between paths. Must be the same across subjects.
- -o, --outdir
Absolute path to a directory to save results in.
- -n, --folder_name
Name of output folder. That contains within it the nfact_pp, nfact_decomp and nfact_dr folders. Default is nfact
- -c, --config
Provide an nfact_config file instead of using command line arguements. Configuration files provide control over all parameters of modules and can be created using nfact_config -C. If this is provided no other arguments are needed to run nfact as arguments are taken from config file rather than command line.
- -P, --pp_skip
Skips nfact_pp. Pipeline still assumes that data has been pre-processed with nfact_pp before. If data hasn’t been pre-processed with nfact_pp consider runing modules seperately
- -Q, --qc_skip
Skips nfact_Qc.
- -D, --dr_skip
Skips nfact_dr so no dual regression is performed.
- -O, --overwrite
Overwirte existing file structure
- nfact_pp inputs:
- -w, --warps
Relative path to warps inside a subjects directory. Include a space between paths. Must be the same across subjects.
- -b, --bpx
Relative path to Bedpostx folder inside a subjects directory. Must be the same across subjects
- -r, --roi
REQUIRED FOR SURFACE MODE: Relative path to a single ROI or multiple ROIS to restrict seeding to (e.g. medial wall masks). Must be the same across subject. ROIS must match number of seeds.
- -f, --file_tree
Use this option to provide name of predefined file tree to perform whole brain tractography. nfact_pp currently comes with HCP filetree. See documentation for further information.
- -sr, --seedref
Absolute path to a reference volume to define seed space used by probtrackx. Default is MNI152 T1 2mm.
- -t, --target
Absolute path to a target image. If not provided will use the seedref.
- nfact_decomp/nfact_dr inputs:
- -d, --dim
This is compulsory option. Number of dimensions/components to retain after running NMF/ICA.
- -a, --algo
Which decomposition algorithm to run. Options are: NMF (default), or ICA. This is case insensitive
- -rf, --rf_decomp
Absolute path to a text file containing the absolute path ROI(s) paths to restrict seeding to (e.g. medial wall masks). This is not needed if seeds are not surfaces. If used nfact_pp then this is the roi_for_decomp.txt file in the nfact_pp directory. This option is not needed if the pipeline is being ran from nfact_pp onwards.
- nfact_Qc inputs:
- --threshold
Z score value to threshold hitmaps.
Example Usage
From command line:
nfact --list_of_subject /absolute path/sub_list \
--seed thalamus.nii.gz \
--algo NMF \
--dim 100 \
--outdir /absolute path/save directory \
--warps standard2acpc_dc.nii.gz acpc_dc2standard.nii.gz \
--ref $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz \
--bpx Diffusion.bedpostX
With a config file:
nfact –config /absolute path/nfact_config.config