diff --git a/fsl/scripts/extract_noise.py b/fsl/scripts/extract_noise.py
new file mode 100644
index 0000000000000000000000000000000000000000..de479d0ce0df4388e5b7ad0abb6bd35a459af5bb
--- /dev/null
+++ b/fsl/scripts/extract_noise.py
@@ -0,0 +1,213 @@
+#!/usr/bin/env python
+#
+# extract_noise.py - Extract ICA component time courses from a MELODIC
+# directory.
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""
+"""
+
+
+from __future__ import print_function
+
+import os.path as op
+import sys
+import argparse
+import warnings
+
+import numpy as np
+
+# See atlasq.py for explanation
+with warnings.catch_warnings():
+ warnings.filterwarnings("ignore", category=FutureWarning)
+
+ import fsl.data.fixlabels as fixlabels
+ import fsl.data.melodicanalysis as melanalysis
+
+
+DTYPE = np.float64
+
+
+usage = """
+Usage:
+ extract_noise <.ica directory> [-o outfile] <fixfile>
+ extract_noise <.ica directory> [-o outfile] <component> [<component> ...]
+""".strip()
+
+
+desc = 'Extract component time series from a MELODIC .ica directory'
+
+
+helps = {
+ 'outfile' :
+ 'File to save time series to',
+
+ 'overwrite' :
+ 'Overwrite output file if it exists',
+
+ 'icadir' :
+ '.ica directory to extract time series from.',
+
+ 'component' :
+ 'Component number or FIX/AROMA file specifying components to extract.',
+
+ 'confound' :
+ 'Extra files to append to output file.',
+}
+
+
+def parseArgs(args):
+ """Parses command line arguments.
+
+ :arg args: Sequence of command line arguments.
+ :returns: An ``argparse.Namespace`` object containing parsed arguments.
+ """
+
+ if len(args) == 0:
+ print(usage)
+ sys.exit(0)
+
+ parser = argparse.ArgumentParser(prog='extract_noise',
+ usage=usage,
+ description=desc)
+
+ parser.add_argument('-o', '--outfile',
+ help=helps['outfile'],
+ default='confound_timeseries.txt')
+ parser.add_argument('-ow', '--overwrite',
+ action='store_true',
+ help=helps['overwrite'])
+ parser.add_argument('-c', '--conffile',
+ action='append',
+ help=helps['confound'])
+ parser.add_argument('icadir',
+ help=helps['icadir'])
+ parser.add_argument('components',
+ nargs='+',
+ help=helps['component'])
+
+ args = parser.parse_args(args)
+
+ # Error if ica directory does not exist
+ if not op.exists(args.icadir):
+ print('ICA directory {} does not exist'.format(args.icadir))
+ sys.exit(1)
+
+ # Error if output exists, but overwrite not specified
+ if op.exists(args.outfile) and not args.overwrite:
+ print('Output file {} already exists and --overwrite not '
+ 'specified'.format(args.outfile))
+ sys.exit(1)
+
+ # Convert components into integers,
+ # or absolute file paths, and error
+ # if any are not one of these.
+ for i, c in enumerate(args.components):
+ if op.exists(c):
+ args.components[i] = op.abspath(c)
+ else:
+ try:
+ args.components[i] = int(c)
+ except ValueError:
+ print('Bad component: {}. Components must either be component '
+ 'indices (starting from 1), or paths to FIX/AROMA '
+ 'files.')
+ sys.exit(1)
+
+ # Convert confound files to absolute
+ # paths, error if any do not exist.
+ for i, cf in enumerate(args.conffile):
+ if not op.exists(cf):
+ print('Confound file does not exist: {}'.format(cf))
+ sys.exit(1)
+ args.conffile[i] = op.abspath(cf)
+
+ args.outfile = op.abspath(args.outfile)
+ args.icadir = op.abspath(args.icadir)
+
+ return args
+
+
+def genComponentIndexList(comps):
+ """
+ """
+
+ allcomps = []
+
+ for c in comps:
+ if isinstance(c, int):
+ ccomps = [c]
+ else:
+ ccomps = fixlabels.loadLabelFile(c, returnIndices=True)[2]
+
+ allcomps.extend([cc - 1 for cc in ccomps])
+
+ return list(sorted(set(allcomps)))
+
+
+def loadConfoundFiles(conffiles, npts):
+ """
+ """
+
+ matrices = []
+
+ for cfile in conffiles:
+
+ mat = np.loadtxt(cfile, dtype=DTYPE)
+
+ if len(mat.shape) == 1:
+ mat = np.atleast_2d(mat).T
+
+ if mat.shape[0] != npts:
+ print('Warning: confound file {} does not have correct number of '
+ 'points (expected {}, has {}). Output will be truncated or '
+ 'padded with NaNs.'.format(cfile, npts, mat.shape[1]))
+ matrices.append(mat)
+
+ totalcols = sum([m.shape[0] for m in matrices])
+ confounds = np.zeros((npts, totalcols), dtype=DTYPE)
+
+ coli = 0
+ for mat in matrices:
+ ncols = mat.shape[1]
+
+ # too many timepoints - truncate
+ if mat.shape[0] > npts:
+ mat = mat[:npts, :]
+
+ # too few timepoints - pad with NaN
+ elif mat.shape[0] < npts:
+ tmat = mat
+ mat = np.zeros((npts, ncols), dtype=DTYPE)
+ mat[:npts, :] = tmat
+ mat[ npts:, :] = np.nan
+
+ confounds[:, coli:coli + ncols] = mat
+ coli = coli + ncols
+
+ return confounds
+
+
+def main(argv=None):
+ """Entry point for the ``extract_noise`` script.
+
+ Identifies component time series to extract, extracts them, loads extra
+ confound files, and saves them out to a file.
+ """
+
+ if argv is None:
+ argv = sys.argv[1:]
+
+ args = parseArgs(argv)
+ comps = genComponentIndexList(args.components)
+ ts = melanalysis.getComponentTimeSeries(args.icadir)
+ ts = ts[:, comps]
+ confs = loadConfoundFiles(args.conffiles, ts.shape[0])
+ ts = np.hstack((ts, confs))
+
+ np.savetxt(args.outfile, ts, fmt='%10.5f')
+
+
+if __name__ == '__main__':
+ sys.exit(main())