def tedana_workflow(data,
tes,
out_dir='.',
mask=None,
fittype='loglin',
combmode='t2s',
tedpca='mdl',
fixed_seed=42,
maxit=500,
maxrestart=10,
tedort=False,
gscontrol=None,
no_png=False,
png_cmap='coolwarm',
verbose=False,
low_mem=False,
debug=False,
quiet=False,
t2smap=None,
mixm=None,
ctab=None,
manacc=None):
"""
Run the "canonical" TE-Dependent ANAlysis workflow.
Parameters
----------
data : :obj:`str` or :obj:`list` of :obj:`str`
Either a single z-concatenated file (single-entry list or str) or a
list of echo-specific files, in ascending order.
tes : :obj:`list`
List of echo times associated with data in milliseconds.
out_dir : :obj:`str`, optional
Output directory.
mask : :obj:`str` or None, optional
Binary mask of voxels to include in TE Dependent ANAlysis. Must be
spatially aligned with `data`. If an explicit mask is not provided,
then Nilearn's compute_epi_mask function will be used to derive a mask
from the first echo's data.
fittype : {'loglin', 'curvefit'}, optional
Monoexponential fitting method. 'loglin' uses the the default linear
fit to the log of the data. 'curvefit' uses a monoexponential fit to
the raw data, which is slightly slower but may be more accurate.
Default is 'loglin'.
combmode : {'t2s'}, optional
Combination scheme for TEs: 't2s' (Posse 1999, default).
tedpca : {'kundu', 'kundu-stabilize', 'mdl', 'aic', 'kic'}, optional
Method with which to select components in TEDPCA. Default is 'mdl'.
tedort : :obj:`bool`, optional
Orthogonalize rejected components w.r.t. accepted ones prior to
denoising. Default is False.
gscontrol : {None, 't1c', 'gsr'} or :obj:`list`, optional
Perform additional denoising to remove spatially diffuse noise. Default
is None.
verbose : :obj:`bool`, optional
Generate intermediate and additional files. Default is False.
no_png : obj:'bool', optional
Do not generate .png plots and figures. Default is false.
png_cmap : obj:'str', optional
Name of a matplotlib colormap to be used when generating figures.
Cannot be used with --no-png. Default is 'coolwarm'.
t2smap : :obj:`str`, optional
Precalculated T2* map in the same space as the input data.
mixm : :obj:`str` or None, optional
File containing mixing matrix, to be used when re-running the workflow.
If not provided, ME-PCA and ME-ICA are done. Default is None.
ctab : :obj:`str` or None, optional
File containing component table from which to extract pre-computed
classifications, to be used with 'mixm' when re-running the workflow.
Default is None.
manacc : :obj:`list`, :obj:`str`, or None, optional
List of manually accepted components. Can be a list of the components,
a comma-separated string with component numbers, or None. Default is
None.
Other Parameters
----------------
fixed_seed : :obj:`int`, optional
Value passed to ``mdp.numx_rand.seed()``.
Set to a positive integer value for reproducible ICA results;
otherwise, set to -1 for varying results across calls.
maxit : :obj:`int`, optional
Maximum number of iterations for ICA. Default is 500.
maxrestart : :obj:`int`, optional
Maximum number of attempts for ICA. If ICA fails to converge, the
fixed seed will be updated and ICA will be run again. If convergence
is achieved before maxrestart attempts, ICA will finish early.
Default is 10.
low_mem : :obj:`bool`, optional
Enables low-memory processing, including the use of IncrementalPCA.
May increase workflow duration. Default is False.
debug : :obj:`bool`, optional
Whether to run in debugging mode or not. Default is False.
quiet : :obj:`bool`, optional
If True, suppresses logging/printing of messages. Default is False.
Notes
-----
This workflow writes out several files. For a complete list of the files
generated by this workflow, please visit
https://tedana.readthedocs.io/en/latest/outputs.html
"""
out_dir = op.abspath(out_dir)
if not op.isdir(out_dir):
os.mkdir(out_dir)
# boilerplate
basename = 'report'
extension = 'txt'
repname = op.join(out_dir, (basename + '.' + extension))
repex = op.join(out_dir, (basename + '*'))
previousreps = glob(repex)
previousreps.sort(reverse=True)
for f in previousreps:
previousparts = op.splitext(f)
newname = previousparts[0] + '_old' + previousparts[1]
os.rename(f, newname)
refname = op.join(out_dir, '_references.txt')
# create logfile name
basename = 'tedana_'
extension = 'tsv'
start_time = datetime.datetime.now().strftime('%Y-%m-%dT%H%M%S')
logname = op.join(out_dir, (basename + start_time + '.' + extension))
# set logging format
log_formatter = logging.Formatter(
'%(asctime)s\t%(name)-12s\t%(levelname)-8s\t%(message)s',
datefmt='%Y-%m-%dT%H:%M:%S')
text_formatter = logging.Formatter('%(message)s')
# set up logging file and open it for writing
log_handler = logging.FileHandler(logname)
log_handler.setFormatter(log_formatter)
# Removing handlers after basicConfig doesn't work, so we use filters
# for the relevant handlers themselves.
log_handler.addFilter(ContextFilter())
sh = logging.StreamHandler()
sh.addFilter(ContextFilter())
if quiet:
logging.basicConfig(level=logging.WARNING, handlers=[log_handler, sh])
elif debug:
logging.basicConfig(level=logging.DEBUG, handlers=[log_handler, sh])
else:
logging.basicConfig(level=logging.INFO, handlers=[log_handler, sh])
# Loggers for report and references
rep_handler = logging.FileHandler(repname)
rep_handler.setFormatter(text_formatter)
ref_handler = logging.FileHandler(refname)
ref_handler.setFormatter(text_formatter)
RepLGR.setLevel(logging.INFO)
RepLGR.addHandler(rep_handler)
RepLGR.setLevel(logging.INFO)
RefLGR.addHandler(ref_handler)
LGR.info('Using output directory: {}'.format(out_dir))
# ensure tes are in appropriate format
tes = [float(te) for te in tes]
n_echos = len(tes)
# Coerce gscontrol to list
if not isinstance(gscontrol, list):
gscontrol = [gscontrol]
LGR.info('Loading input data: {}'.format([f for f in data]))
catd, ref_img = io.load_data(data, n_echos=n_echos)
n_samp, n_echos, n_vols = catd.shape
LGR.debug('Resulting data shape: {}'.format(catd.shape))
if no_png and (png_cmap != 'coolwarm'):
LGR.warning('Overriding --no-png since --png-cmap provided.')
no_png = False
# check if TR is 0
img_t_r = ref_img.header.get_zooms()[-1]
if img_t_r == 0 and not no_png:
raise IOError(
'Dataset has a TR of 0. This indicates incorrect'
' header information. To correct this, we recommend'
' using this snippet:'
'\n'
'https://gist.github.com/jbteves/032c87aeb080dd8de8861cb151bff5d6'
'\n'
'to correct your TR to the value it should be.')
if mixm is not None and op.isfile(mixm):
mixm = op.abspath(mixm)
# Allow users to re-run on same folder
if mixm != op.join(out_dir, 'ica_mixing.tsv'):
shutil.copyfile(mixm, op.join(out_dir, 'ica_mixing.tsv'))
shutil.copyfile(mixm, op.join(out_dir, op.basename(mixm)))
elif mixm is not None:
raise IOError('Argument "mixm" must be an existing file.')
if ctab is not None and op.isfile(ctab):
ctab = op.abspath(ctab)
# Allow users to re-run on same folder
if ctab != op.join(out_dir, 'ica_decomposition.json'):
shutil.copyfile(ctab, op.join(out_dir, 'ica_decomposition.json'))
shutil.copyfile(ctab, op.join(out_dir, op.basename(ctab)))
elif ctab is not None:
raise IOError('Argument "ctab" must be an existing file.')
if isinstance(manacc, str):
manacc = [int(comp) for comp in manacc.split(',')]
if ctab and not mixm:
LGR.warning('Argument "ctab" requires argument "mixm".')
ctab = None
elif manacc is not None and not mixm:
LGR.warning('Argument "manacc" requires argument "mixm".')
manacc = None
if t2smap is not None and op.isfile(t2smap):
t2smap = op.abspath(t2smap)
# Allow users to re-run on same folder
if t2smap != op.join(out_dir, 't2sv.nii.gz'):
shutil.copyfile(t2smap, op.join(out_dir, 't2sv.nii.gz'))
shutil.copyfile(t2smap, op.join(out_dir, op.basename(t2smap)))
elif t2smap is not None:
raise IOError('Argument "t2smap" must be an existing file.')
RepLGR.info("TE-dependence analysis was performed on input data.")
if mask and not t2smap:
# TODO: add affine check
LGR.info('Using user-defined mask')
RepLGR.info("A user-defined mask was applied to the data.")
elif t2smap and not mask:
LGR.info('Using user-defined T2* map to generate mask')
t2s_limited = utils.load_image(t2smap)
t2s_full = t2s_limited.copy()
mask = (t2s_limited != 0).astype(int)
elif t2smap and mask:
LGR.info('Combining user-defined mask and T2* map to generate mask')
t2s_limited = utils.load_image(t2smap)
t2s_full = t2s_limited.copy()
mask = utils.load_image(mask)
mask[t2s_limited == 0] = 0 # reduce mask based on T2* map
else:
LGR.info('Computing EPI mask from first echo')
first_echo_img = io.new_nii_like(ref_img, catd[:, 0, :])
mask = compute_epi_mask(first_echo_img)
RepLGR.info("An initial mask was generated from the first echo using "
"nilearn's compute_epi_mask function.")
mask, masksum = utils.make_adaptive_mask(catd, mask=mask, getsum=True)
LGR.debug('Retaining {}/{} samples'.format(mask.sum(), n_samp))
io.filewrite(masksum, op.join(out_dir, 'adaptive_mask.nii'), ref_img)
if t2smap is None:
LGR.info('Computing T2* map')
t2s_limited, s0_limited, t2s_full, s0_full = decay.fit_decay(
catd, tes, mask, masksum, fittype)
# set a hard cap for the T2* map
# anything that is 10x higher than the 99.5 %ile will be reset to 99.5 %ile
cap_t2s = stats.scoreatpercentile(t2s_limited.flatten(),
99.5,
interpolation_method='lower')
LGR.debug('Setting cap on T2* map at {:.5f}'.format(cap_t2s * 10))
t2s_limited[t2s_limited > cap_t2s * 10] = cap_t2s
io.filewrite(t2s_limited, op.join(out_dir, 't2sv.nii'), ref_img)
io.filewrite(s0_limited, op.join(out_dir, 's0v.nii'), ref_img)
if verbose:
io.filewrite(t2s_full, op.join(out_dir, 't2svG.nii'), ref_img)
io.filewrite(s0_full, op.join(out_dir, 's0vG.nii'), ref_img)
# optimally combine data
data_oc = combine.make_optcom(catd,
tes,
mask,
t2s=t2s_full,
combmode=combmode)
# regress out global signal unless explicitly not desired
if 'gsr' in gscontrol:
catd, data_oc = gsc.gscontrol_raw(catd,
data_oc,
n_echos,
ref_img,
out_dir=out_dir)
if mixm is None:
# Identify and remove thermal noise from data
dd, n_components = decomposition.tedpca(catd,
data_oc,
combmode,
mask,
t2s_limited,
t2s_full,
ref_img,
tes=tes,
algorithm=tedpca,
kdaw=10.,
rdaw=1.,
out_dir=out_dir,
verbose=verbose,
low_mem=low_mem)
mmix_orig = decomposition.tedica(dd, n_components, fixed_seed, maxit,
maxrestart)
if verbose:
io.filewrite(utils.unmask(dd, mask),
op.join(out_dir, 'ts_OC_whitened.nii.gz'), ref_img)
LGR.info('Making second component selection guess from ICA results')
# Estimate betas and compute selection metrics for mixing matrix
# generated from dimensionally reduced data using full data (i.e., data
# with thermal noise)
comptable, metric_maps, betas, mmix = metrics.dependence_metrics(
catd,
data_oc,
mmix_orig,
t2s_limited,
tes,
ref_img,
reindex=True,
label='meica_',
out_dir=out_dir,
algorithm='kundu_v2',
verbose=verbose)
comp_names = [
io.add_decomp_prefix(comp,
prefix='ica',
max_value=comptable.index.max())
for comp in comptable.index.values
]
mixing_df = pd.DataFrame(data=mmix, columns=comp_names)
mixing_df.to_csv(op.join(out_dir, 'ica_mixing.tsv'),
sep='\t',
index=False)
betas_oc = utils.unmask(computefeats2(data_oc, mmix, mask), mask)
io.filewrite(betas_oc, op.join(out_dir, 'ica_components.nii.gz'),
ref_img)
comptable = metrics.kundu_metrics(comptable, metric_maps)
comptable = selection.kundu_selection_v2(comptable, n_echos, n_vols)
else:
LGR.info('Using supplied mixing matrix from ICA')
mmix_orig = pd.read_table(op.join(out_dir, 'ica_mixing.tsv')).values
if ctab is None:
comptable, metric_maps, betas, mmix = metrics.dependence_metrics(
catd,
data_oc,
mmix_orig,
t2s_limited,
tes,
ref_img,
label='meica_',
out_dir=out_dir,
algorithm='kundu_v2',
verbose=verbose)
comptable = metrics.kundu_metrics(comptable, metric_maps)
comptable = selection.kundu_selection_v2(comptable, n_echos,
n_vols)
else:
mmix = mmix_orig.copy()
comptable = io.load_comptable(ctab)
if manacc is not None:
comptable = selection.manual_selection(comptable, acc=manacc)
betas_oc = utils.unmask(computefeats2(data_oc, mmix, mask), mask)
io.filewrite(betas_oc, op.join(out_dir, 'ica_components.nii.gz'),
ref_img)
# Save decomposition
comptable[
'Description'] = 'ICA fit to dimensionally-reduced optimally combined data.'
mmix_dict = {}
mmix_dict['Method'] = ('Independent components analysis with FastICA '
'algorithm implemented by sklearn. Components '
'are sorted by Kappa in descending order. '
'Component signs are flipped to best match the '
'data.')
io.save_comptable(comptable,
op.join(out_dir, 'ica_decomposition.json'),
label='ica',
metadata=mmix_dict)
if comptable[comptable.classification == 'accepted'].shape[0] == 0:
LGR.warning('No BOLD components detected! Please check data and '
'results!')
mmix_orig = mmix.copy()
if tedort:
acc_idx = comptable.loc[~comptable.classification.str.
contains('rejected')].index.values
rej_idx = comptable.loc[comptable.classification.str.contains(
'rejected')].index.values
acc_ts = mmix[:, acc_idx]
rej_ts = mmix[:, rej_idx]
betas = np.linalg.lstsq(acc_ts, rej_ts, rcond=None)[0]
pred_rej_ts = np.dot(acc_ts, betas)
resid = rej_ts - pred_rej_ts
mmix[:, rej_idx] = resid
comp_names = [
io.add_decomp_prefix(comp,
prefix='ica',
max_value=comptable.index.max())
for comp in comptable.index.values
]
mixing_df = pd.DataFrame(data=mmix, columns=comp_names)
mixing_df.to_csv(op.join(out_dir, 'ica_orth_mixing.tsv'),
sep='\t',
index=False)
RepLGR.info("Rejected components' time series were then "
"orthogonalized with respect to accepted components' time "
"series.")
io.writeresults(data_oc,
mask=mask,
comptable=comptable,
mmix=mmix,
n_vols=n_vols,
ref_img=ref_img,
out_dir=out_dir)
if 't1c' in gscontrol:
gsc.gscontrol_mmix(data_oc,
mmix,
mask,
comptable,
ref_img,
out_dir=out_dir)
if verbose:
io.writeresults_echoes(catd,
mmix,
mask,
comptable,
ref_img,
out_dir=out_dir)
if not no_png:
LGR.info('Making figures folder with static component maps and '
'timecourse plots.')
# make figure folder first
if not op.isdir(op.join(out_dir, 'figures')):
os.mkdir(op.join(out_dir, 'figures'))
viz.write_comp_figs(data_oc,
mask=mask,
comptable=comptable,
mmix=mmix_orig,
ref_img=ref_img,
out_dir=op.join(out_dir, 'figures'),
png_cmap=png_cmap)
LGR.info('Making Kappa vs Rho scatter plot')
viz.write_kappa_scatter(comptable=comptable,
out_dir=op.join(out_dir, 'figures'))
LGR.info('Making Kappa/Rho scree plot')
viz.write_kappa_scree(comptable=comptable,
out_dir=op.join(out_dir, 'figures'))
LGR.info('Making overall summary figure')
viz.write_summary_fig(comptable=comptable,
out_dir=op.join(out_dir, 'figures'))
LGR.info('Workflow completed')
RepLGR.info("This workflow used numpy (Van Der Walt, Colbert, & "
"Varoquaux, 2011), scipy (Jones et al., 2001), pandas "
"(McKinney, 2010), scikit-learn (Pedregosa et al., 2011), "
"nilearn, and nibabel (Brett et al., 2019).")
RefLGR.info(
"Van Der Walt, S., Colbert, S. C., & Varoquaux, G. (2011). The "
"NumPy array: a structure for efficient numerical computation. "
"Computing in Science & Engineering, 13(2), 22.")
RefLGR.info("Jones E, Oliphant E, Peterson P, et al. SciPy: Open Source "
"Scientific Tools for Python, 2001-, http://www.scipy.org/")
RefLGR.info("McKinney, W. (2010, June). Data structures for statistical "
"computing in python. In Proceedings of the 9th Python in "
"Science Conference (Vol. 445, pp. 51-56).")
RefLGR.info("Pedregosa, F., Varoquaux, G., Gramfort, A., Michel, V., "
"Thirion, B., Grisel, O., ... & Vanderplas, J. (2011). "
"Scikit-learn: Machine learning in Python. Journal of machine "
"learning research, 12(Oct), 2825-2830.")
RefLGR.info("Brett, M., Markiewicz, C. J., Hanke, M., Côté, M.-A., "
"Cipollini, B., McCarthy, P., … freec84. (2019, May 28). "
"nipy/nibabel. Zenodo. http://doi.org/10.5281/zenodo.3233118")
RepLGR.info("This workflow also used the Dice similarity index "
"(Dice, 1945; Sørensen, 1948).")
RefLGR.info("Dice, L. R. (1945). Measures of the amount of ecologic "
"association between species. Ecology, 26(3), 297-302.")
RefLGR.info(
"Sørensen, T. J. (1948). A method of establishing groups of "
"equal amplitude in plant sociology based on similarity of "
"species content and its application to analyses of the "
"vegetation on Danish commons. I kommission hos E. Munksgaard.")
with open(repname, 'r') as fo:
report = [line.rstrip() for line in fo.readlines()]
report = ' '.join(report)
with open(refname, 'r') as fo:
reference_list = sorted(list(set(fo.readlines())))
references = '\n'.join(reference_list)
report += '\n\nReferences\n' + references
with open(repname, 'w') as fo:
fo.write(report)
os.remove(refname)
for handler in logging.root.handlers[:]:
logging.root.removeHandler(handler)
def tedpca(data_cat,
data_oc,
combmode,
mask,
adaptive_mask,
t2sG,
ref_img,
tes,
algorithm='mdl',
kdaw=10.,
rdaw=1.,
out_dir='.',
verbose=False,
low_mem=False):
"""
Use principal components analysis (PCA) to identify and remove thermal
noise from multi-echo data.
Parameters
----------
data_cat : (S x E x T) array_like
Input functional data
data_oc : (S x T) array_like
Optimally combined time series data
combmode : {'t2s', 'paid'} str
How optimal combination of echos should be made, where 't2s' indicates
using the method of Posse 1999 and 'paid' indicates using the method of
Poser 2006
mask : (S,) array_like
Boolean mask array
adaptive_mask : (S,) array_like
Array where each value indicates the number of echoes with good signal
for that voxel. This mask may be thresholded; for example, with values
less than 3 set to 0.
For more information on thresholding, see `make_adaptive_mask`.
t2sG : (S,) array_like
Map of voxel-wise T2* estimates.
ref_img : :obj:`str` or img_like
Reference image to dictate how outputs are saved to disk
tes : :obj:`list`
List of echo times associated with `data_cat`, in milliseconds
algorithm : {'kundu', 'kundu-stabilize', 'mdl', 'aic', 'kic', float}, optional
Method with which to select components in TEDPCA. PCA
decomposition with the mdl, kic and aic options are based on a Moving Average
(stationary Gaussian) process and are ordered from most to least aggressive
(see Li et al., 2007).
If a float is provided, then it is assumed to represent percentage of variance
explained (0-1) to retain from PCA.
Default is 'mdl'.
kdaw : :obj:`float`, optional
Dimensionality augmentation weight for Kappa calculations. Must be a
non-negative float, or -1 (a special value). Default is 10.
rdaw : :obj:`float`, optional
Dimensionality augmentation weight for Rho calculations. Must be a
non-negative float, or -1 (a special value). Default is 1.
out_dir : :obj:`str`, optional
Output directory.
verbose : :obj:`bool`, optional
Whether to output files from fitmodels_direct or not. Default: False
low_mem : :obj:`bool`, optional
Whether to use incremental PCA (for low-memory systems) or not.
This is only compatible with the "kundu" or "kundu-stabilize" algorithms.
Default: False
Returns
-------
kept_data : (S x T) :obj:`numpy.ndarray`
Dimensionally reduced optimally combined functional data
n_components : :obj:`int`
Number of components retained from PCA decomposition
Notes
-----
====================== =================================================
Notation Meaning
====================== =================================================
:math:`\\kappa` Component pseudo-F statistic for TE-dependent
(BOLD) model.
:math:`\\rho` Component pseudo-F statistic for TE-independent
(artifact) model.
:math:`v` Voxel
:math:`V` Total number of voxels in mask
:math:`\\zeta` Something
:math:`c` Component
:math:`p` Something else
====================== =================================================
Steps:
1. Variance normalize either multi-echo or optimally combined data,
depending on settings.
2. Decompose normalized data using PCA or SVD.
3. Compute :math:`{\\kappa}` and :math:`{\\rho}`:
.. math::
{\\kappa}_c = \\frac{\\sum_{v}^V {\\zeta}_{c,v}^p * \
F_{c,v,R_2^*}}{\\sum {\\zeta}_{c,v}^p}
{\\rho}_c = \\frac{\\sum_{v}^V {\\zeta}_{c,v}^p * \
F_{c,v,S_0}}{\\sum {\\zeta}_{c,v}^p}
4. Some other stuff. Something about elbows.
5. Classify components as thermal noise if they meet both of the
following criteria:
- Nonsignificant :math:`{\\kappa}` and :math:`{\\rho}`.
- Nonsignificant variance explained.
Outputs:
This function writes out several files:
====================== =================================================
Filename Content
====================== =================================================
pca_decomposition.json PCA component table.
pca_mixing.tsv PCA mixing matrix.
pca_components.nii.gz Component weight maps.
====================== =================================================
See Also
--------
:func:`tedana.utils.make_adaptive_mask` : The function used to create the ``adaptive_mask``
parameter.
"""
if algorithm == 'kundu':
alg_str = ("followed by the Kundu component selection decision "
"tree (Kundu et al., 2013)")
RefLGR.info("Kundu, P., Brenowitz, N. D., Voon, V., Worbe, Y., "
"Vértes, P. E., Inati, S. J., ... & Bullmore, E. T. "
"(2013). Integrated strategy for improving functional "
"connectivity mapping using multiecho fMRI. Proceedings "
"of the National Academy of Sciences, 110(40), "
"16187-16192.")
elif algorithm == 'kundu-stabilize':
alg_str = ("followed by the 'stabilized' Kundu component "
"selection decision tree (Kundu et al., 2013)")
RefLGR.info("Kundu, P., Brenowitz, N. D., Voon, V., Worbe, Y., "
"Vértes, P. E., Inati, S. J., ... & Bullmore, E. T. "
"(2013). Integrated strategy for improving functional "
"connectivity mapping using multiecho fMRI. Proceedings "
"of the National Academy of Sciences, 110(40), "
"16187-16192.")
elif isinstance(algorithm, Number):
alg_str = (
"in which the number of components was determined based on a "
"variance explained threshold")
else:
alg_str = (
"based on the PCA component estimation with a Moving Average"
"(stationary Gaussian) process (Li et al., 2007)")
RefLGR.info("Li, Y.O., Adalı, T. and Calhoun, V.D., (2007). "
"Estimating the number of independent components for "
"functional magnetic resonance imaging data. "
"Human brain mapping, 28(11), pp.1251-1266.")
RepLGR.info("Principal component analysis {0} was applied to "
"the optimally combined data for dimensionality "
"reduction.".format(alg_str))
n_samp, n_echos, n_vols = data_cat.shape
LGR.info('Computing PCA of optimally combined multi-echo data')
data = data_oc[mask, :]
data_z = ((data.T - data.T.mean(axis=0)) /
data.T.std(axis=0)).T # var normalize ts
data_z = (data_z -
data_z.mean()) / data_z.std() # var normalize everything
if algorithm in ['mdl', 'aic', 'kic']:
data_img = io.new_nii_like(ref_img, utils.unmask(data, mask))
mask_img = io.new_nii_like(ref_img, mask.astype(int))
voxel_comp_weights, varex, varex_norm, comp_ts = ma_pca.ma_pca(
data_img, mask_img, algorithm)
elif isinstance(algorithm, Number):
ppca = PCA(copy=False, n_components=algorithm, svd_solver="full")
ppca.fit(data_z)
comp_ts = ppca.components_.T
varex = ppca.explained_variance_
voxel_comp_weights = np.dot(np.dot(data_z, comp_ts),
np.diag(1. / varex))
varex_norm = varex / varex.sum()
elif low_mem:
voxel_comp_weights, varex, comp_ts = low_mem_pca(data_z)
varex_norm = varex / varex.sum()
else:
ppca = PCA(copy=False, n_components=(n_vols - 1))
ppca.fit(data_z)
comp_ts = ppca.components_.T
varex = ppca.explained_variance_
voxel_comp_weights = np.dot(np.dot(data_z, comp_ts),
np.diag(1. / varex))
varex_norm = varex / varex.sum()
# Compute Kappa and Rho for PCA comps
# Normalize each component's time series
vTmixN = stats.zscore(comp_ts, axis=0)
comptable, _, _, _ = metrics.dependence_metrics(data_cat,
data_oc,
comp_ts,
adaptive_mask,
tes,
ref_img,
reindex=False,
mmixN=vTmixN,
algorithm=None,
label='mepca_',
out_dir=out_dir,
verbose=verbose)
# varex_norm from PCA overrides varex_norm from dependence_metrics,
# but we retain the original
comptable['estimated normalized variance explained'] = \
comptable['normalized variance explained']
comptable['normalized variance explained'] = varex_norm
# write component maps to 4D image
comp_ts_z = stats.zscore(comp_ts, axis=0)
comp_maps = utils.unmask(computefeats2(data_oc, comp_ts_z, mask), mask)
io.filewrite(comp_maps, op.join(out_dir, 'pca_components.nii.gz'), ref_img)
# Select components using decision tree
if algorithm == 'kundu':
comptable = kundu_tedpca(comptable,
n_echos,
kdaw,
rdaw,
stabilize=False)
elif algorithm == 'kundu-stabilize':
comptable = kundu_tedpca(comptable,
n_echos,
kdaw,
rdaw,
stabilize=True)
else:
alg_str = "variance explained-based" if isinstance(
algorithm, Number) else algorithm
LGR.info('Selected {0} components with {1} dimensionality '
'detection'.format(comptable.shape[0], alg_str))
comptable['classification'] = 'accepted'
comptable['rationale'] = ''
# Save decomposition
comp_names = [
io.add_decomp_prefix(comp,
prefix='pca',
max_value=comptable.index.max())
for comp in comptable.index.values
]
mixing_df = pd.DataFrame(data=comp_ts, columns=comp_names)
mixing_df.to_csv(op.join(out_dir, 'pca_mixing.tsv'), sep='\t', index=False)
comptable['Description'] = 'PCA fit to optimally combined data.'
mmix_dict = {}
mmix_dict['Method'] = ('Principal components analysis implemented by '
'sklearn. Components are sorted by variance '
'explained in descending order. '
'Component signs are flipped to best match the '
'data.')
io.save_comptable(comptable,
op.join(out_dir, 'pca_decomposition.json'),
label='pca',
metadata=mmix_dict)
acc = comptable[comptable.classification == 'accepted'].index.values
n_components = acc.size
voxel_kept_comp_weighted = (voxel_comp_weights[:, acc] * varex[None, acc])
kept_data = np.dot(voxel_kept_comp_weighted, comp_ts[:, acc].T)
kept_data = stats.zscore(kept_data,
axis=1) # variance normalize time series
kept_data = stats.zscore(kept_data,
axis=None) # variance normalize everything
return kept_data, n_components
def tedpca(data_cat, data_oc, combmode, mask, t2s, t2sG,
ref_img, tes, algorithm='mdl', source_tes=-1, kdaw=10., rdaw=1.,
out_dir='.', verbose=False, low_mem=False):
"""
Use principal components analysis (PCA) to identify and remove thermal
noise from multi-echo data.
Parameters
----------
data_cat : (S x E x T) array_like
Input functional data
data_oc : (S x T) array_like
Optimally combined time series data
combmode : {'t2s', 'paid'} str
How optimal combination of echos should be made, where 't2s' indicates
using the method of Posse 1999 and 'paid' indicates using the method of
Poser 2006
mask : (S,) array_like
Boolean mask array
t2s : (S,) array_like
Map of voxel-wise T2* estimates.
t2sG : (S,) array_like
Map of voxel-wise T2* estimates.
ref_img : :obj:`str` or img_like
Reference image to dictate how outputs are saved to disk
tes : :obj:`list`
List of echo times associated with `data_cat`, in milliseconds
algorithm : {'mle', 'kundu', 'kundu-stabilize', 'mdl', 'aic', 'kic'}, optional
Method with which to select components in TEDPCA. Default is 'mdl'. PCA
decomposition with the mdl, kic and aic options are based on a Moving Average
(stationary Gaussian) process and are ordered from most to least aggresive.
See (Li et al., 2007).
source_tes : :obj:`int` or :obj:`list` of :obj:`int`, optional
Which echos to use in PCA. Values -1 and 0 are special, where a value
of -1 will indicate using the optimal combination of the echos
and 0 will indicate using all the echos. A list can be provided
to indicate a subset of echos.
Default: -1
kdaw : :obj:`float`, optional
Dimensionality augmentation weight for Kappa calculations. Must be a
non-negative float, or -1 (a special value). Default is 10.
rdaw : :obj:`float`, optional
Dimensionality augmentation weight for Rho calculations. Must be a
non-negative float, or -1 (a special value). Default is 1.
out_dir : :obj:`str`, optional
Output directory.
verbose : :obj:`bool`, optional
Whether to output files from fitmodels_direct or not. Default: False
low_mem : :obj:`bool`, optional
Whether to use incremental PCA (for low-memory systems) or not.
Default: False
Returns
-------
kept_data : (S x T) :obj:`numpy.ndarray`
Dimensionally reduced optimally combined functional data
n_components : :obj:`int`
Number of components retained from PCA decomposition
Notes
-----
====================== =================================================
Notation Meaning
====================== =================================================
:math:`\\kappa` Component pseudo-F statistic for TE-dependent
(BOLD) model.
:math:`\\rho` Component pseudo-F statistic for TE-independent
(artifact) model.
:math:`v` Voxel
:math:`V` Total number of voxels in mask
:math:`\\zeta` Something
:math:`c` Component
:math:`p` Something else
====================== =================================================
Steps:
1. Variance normalize either multi-echo or optimally combined data,
depending on settings.
2. Decompose normalized data using PCA or SVD.
3. Compute :math:`{\\kappa}` and :math:`{\\rho}`:
.. math::
{\\kappa}_c = \\frac{\\sum_{v}^V {\\zeta}_{c,v}^p * \
F_{c,v,R_2^*}}{\\sum {\\zeta}_{c,v}^p}
{\\rho}_c = \\frac{\\sum_{v}^V {\\zeta}_{c,v}^p * \
F_{c,v,S_0}}{\\sum {\\zeta}_{c,v}^p}
4. Some other stuff. Something about elbows.
5. Classify components as thermal noise if they meet both of the
following criteria:
- Nonsignificant :math:`{\\kappa}` and :math:`{\\rho}`.
- Nonsignificant variance explained.
Outputs:
This function writes out several files:
====================== =================================================
Filename Content
====================== =================================================
pca_decomposition.json PCA component table.
pca_mixing.tsv PCA mixing matrix.
pca_components.nii.gz Component weight maps.
====================== =================================================
"""
if low_mem and algorithm == 'mle':
LGR.warning('Low memory option is not compatible with MLE '
'dimensionality estimation. Switching to Kundu decision '
'tree.')
algorithm = 'kundu'
if algorithm == 'mle':
alg_str = "using MLE dimensionality estimation (Minka, 2001)"
RefLGR.info("Minka, T. P. (2001). Automatic choice of dimensionality "
"for PCA. In Advances in neural information processing "
"systems (pp. 598-604).")
elif algorithm == 'kundu':
alg_str = ("followed by the Kundu component selection decision "
"tree (Kundu et al., 2013)")
RefLGR.info("Kundu, P., Brenowitz, N. D., Voon, V., Worbe, Y., "
"Vértes, P. E., Inati, S. J., ... & Bullmore, E. T. "
"(2013). Integrated strategy for improving functional "
"connectivity mapping using multiecho fMRI. Proceedings "
"of the National Academy of Sciences, 110(40), "
"16187-16192.")
elif algorithm == 'kundu-stabilize':
alg_str = ("followed by the 'stabilized' Kundu component "
"selection decision tree (Kundu et al., 2013)")
RefLGR.info("Kundu, P., Brenowitz, N. D., Voon, V., Worbe, Y., "
"Vértes, P. E., Inati, S. J., ... & Bullmore, E. T. "
"(2013). Integrated strategy for improving functional "
"connectivity mapping using multiecho fMRI. Proceedings "
"of the National Academy of Sciences, 110(40), "
"16187-16192.")
else:
alg_str = ("based on the PCA component estimation with a Moving Average"
"(stationary Gaussian) process (Li et al., 2007)")
RefLGR.info("Li, Y.O., Adalı, T. and Calhoun, V.D., (2007). "
"Estimating the number of independent components for "
"functional magnetic resonance imaging data. "
"Human brain mapping, 28(11), pp.1251-1266.")
if source_tes == -1:
dat_str = "the optimally combined data"
elif source_tes == 0:
dat_str = "the z-concatenated multi-echo data"
else:
dat_str = "a z-concatenated subset of echoes from the input data"
RepLGR.info("Principal component analysis {0} was applied to "
"{1} for dimensionality reduction.".format(alg_str, dat_str))
n_samp, n_echos, n_vols = data_cat.shape
source_tes = np.array([int(ee) for ee in str(source_tes).split(',')])
if len(source_tes) == 1 and source_tes[0] == -1:
LGR.info('Computing PCA of optimally combined multi-echo data')
data = data_oc[mask, :][:, np.newaxis, :]
elif len(source_tes) == 1 and source_tes[0] == 0:
LGR.info('Computing PCA of spatially concatenated multi-echo data')
data = data_cat[mask, ...]
else:
LGR.info('Computing PCA of echo #{0}'.format(','.join([str(ee) for ee in source_tes])))
data = np.stack([data_cat[mask, ee, :] for ee in source_tes - 1], axis=1)
eim = np.squeeze(_utils.eimask(data))
data = np.squeeze(data[eim])
data_z = ((data.T - data.T.mean(axis=0)) / data.T.std(axis=0)).T # var normalize ts
data_z = (data_z - data_z.mean()) / data_z.std() # var normalize everything
if algorithm in ['mdl', 'aic', 'kic']:
data_img = io.new_nii_like(
ref_img, utils.unmask(utils.unmask(data, eim), mask))
mask_img = io.new_nii_like(ref_img,
utils.unmask(eim, mask).astype(int))
voxel_comp_weights, varex, varex_norm, comp_ts = ma_pca.ma_pca(
data_img, mask_img, algorithm)
elif algorithm == 'mle':
voxel_comp_weights, varex, varex_norm, comp_ts = run_mlepca(data_z)
elif low_mem:
voxel_comp_weights, varex, comp_ts = low_mem_pca(data_z)
varex_norm = varex / varex.sum()
else:
ppca = PCA(copy=False, n_components=(n_vols - 1))
ppca.fit(data_z)
comp_ts = ppca.components_.T
varex = ppca.explained_variance_
voxel_comp_weights = np.dot(np.dot(data_z, comp_ts),
np.diag(1. / varex))
varex_norm = varex / varex.sum()
# Compute Kappa and Rho for PCA comps
eimum = np.atleast_2d(eim)
eimum = np.transpose(eimum, np.argsort(eimum.shape)[::-1])
eimum = eimum.prod(axis=1)
o = np.zeros((mask.shape[0], *eimum.shape[1:]))
o[mask, ...] = eimum
eimum = np.squeeze(o).astype(bool)
# Normalize each component's time series
vTmixN = stats.zscore(comp_ts, axis=0)
comptable, _, _, _ = metrics.dependence_metrics(data_cat,
data_oc,
comp_ts,
t2s,
tes,
ref_img,
reindex=False,
mmixN=vTmixN,
algorithm=None,
label='mepca_',
out_dir=out_dir,
verbose=verbose)
# varex_norm from PCA overrides varex_norm from dependence_metrics,
# but we retain the original
comptable['estimated normalized variance explained'] = \
comptable['normalized variance explained']
comptable['normalized variance explained'] = varex_norm
# write component maps to 4D image
comp_ts_z = stats.zscore(comp_ts, axis=0)
comp_maps = utils.unmask(computefeats2(data_oc, comp_ts_z, mask), mask)
io.filewrite(comp_maps, op.join(out_dir, 'pca_components.nii.gz'), ref_img)
# Select components using decision tree
if algorithm == 'kundu':
comptable = kundu_tedpca(comptable, n_echos, kdaw, rdaw, stabilize=False)
elif algorithm == 'kundu-stabilize':
comptable = kundu_tedpca(comptable, n_echos, kdaw, rdaw, stabilize=True)
elif algorithm == 'mle':
LGR.info('Selected {0} components with MLE dimensionality '
'detection'.format(comptable.shape[0]))
comptable['classification'] = 'accepted'
comptable['rationale'] = ''
elif algorithm in ['mdl', 'aic', 'kic']:
LGR.info('Selected {0} components with {1} dimensionality '
'detection'.format(comptable.shape[0], algorithm))
comptable['classification'] = 'accepted'
comptable['rationale'] = ''
# Save decomposition
comp_names = [io.add_decomp_prefix(comp, prefix='pca', max_value=comptable.index.max())
for comp in comptable.index.values]
mixing_df = pd.DataFrame(data=comp_ts, columns=comp_names)
mixing_df.to_csv(op.join(out_dir, 'pca_mixing.tsv'), sep='\t', index=False)
data_type = 'optimally combined data' if source_tes == -1 else 'z-concatenated data'
comptable['Description'] = 'PCA fit to {0}.'.format(data_type)
mmix_dict = {}
mmix_dict['Method'] = ('Principal components analysis implemented by '
'sklearn. Components are sorted by variance '
'explained in descending order. '
'Component signs are flipped to best match the '
'data.')
io.save_comptable(comptable, op.join(out_dir, 'pca_decomposition.json'),
label='pca', metadata=mmix_dict)
acc = comptable[comptable.classification == 'accepted'].index.values
n_components = acc.size
voxel_kept_comp_weighted = (voxel_comp_weights[:, acc] * varex[None, acc])
kept_data = np.dot(voxel_kept_comp_weighted, comp_ts[:, acc].T)
kept_data = stats.zscore(kept_data, axis=1) # variance normalize time series
kept_data = stats.zscore(kept_data, axis=None) # variance normalize everything
return kept_data, n_components