Add --masktype option to control adaptive mask method

.readthedocs.yml

@@ -6,7 +6,7 @@ sphinx:
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.8"
+    python: "3.10"
   jobs:
     post_checkout:
       - git fetch --unshallow

tedana/tests/test_decay.py

@@ -16,7 +16,7 @@ def testdata1():
     tes = np.array([14.5, 38.5, 62.5])
     in_files = [op.join(get_test_data_path(), f"echo{i + 1}.nii.gz") for i in range(3)]
     data, _ = io.load_data(in_files, n_echos=len(tes))
-    mask, adaptive_mask = utils.make_adaptive_mask(data, getsum=True)
+    mask, adaptive_mask = utils.make_adaptive_mask(data, methods=["dropout", "decay"])
     fittype = "loglin"
     data_dict = {
         "data": data,

tedana/tests/test_integration.py

@@ -669,6 +669,7 @@ def test_integration_t2smap(skip_integration):
         + ["-e"]
         + [str(te) for te in echo_times]
         + ["--out-dir", out_dir, "--fittype", "curvefit"]
+        + ["--masktype", "dropout", "decay"]
     )
     t2smap_cli._main(args)
 

tedana/tests/test_metrics.py

@@ -17,7 +17,7 @@ def testdata1():
     tes = np.array([14.5, 38.5, 62.5])
     in_files = [op.join(get_test_data_path(), f"echo{i + 1}.nii.gz") for i in range(3)]
     data_cat, ref_img = io.load_data(in_files, n_echos=len(tes))
-    _, adaptive_mask = utils.make_adaptive_mask(data_cat, getsum=True)
+    _, adaptive_mask = utils.make_adaptive_mask(data_cat, methods=["dropout", "decay"])
     data_optcom = np.mean(data_cat, axis=1)
     mixing = np.random.random((data_optcom.shape[1], 50))
     io_generator = io.OutputGenerator(ref_img)

tedana/tests/test_utils.py

@@ -75,26 +75,69 @@ def test_reshape_niimg():
 
 
 def test_make_adaptive_mask():
+    """Test tedana.utils.make_adaptive_mask with different methods."""
     # load data make masks
     data = io.load_data(fnames, n_echos=len(tes))[0]
-    mask, masksum = utils.make_adaptive_mask(data, getsum=True, threshold=1)
 
-    # getsum doesn't change mask values
-    assert np.allclose(mask, utils.make_adaptive_mask(data))
-    # shapes are all the same
+    # Just dropout method
+    mask, masksum = utils.make_adaptive_mask(data, threshold=1, methods=["dropout"])
+
     assert mask.shape == masksum.shape == (64350,)
     assert np.allclose(mask, (masksum >= 1).astype(bool))
-    # mask has correct # of entries
     assert mask.sum() == 50786
-    # masksum has correct values
     vals, counts = np.unique(masksum, return_counts=True)
     assert np.allclose(vals, np.array([0, 1, 2, 3]))
     assert np.allclose(counts, np.array([13564, 3977, 5060, 41749]))
 
+    # Just decay method
+    mask, masksum = utils.make_adaptive_mask(data, threshold=1, methods=["decay"])
+
+    assert mask.shape == masksum.shape == (64350,)
+    assert np.allclose(mask, (masksum >= 1).astype(bool))
+    assert mask.sum() == 64350  # This method can't flag first echo as bad
+    vals, counts = np.unique(masksum, return_counts=True)
+    assert np.allclose(vals, np.array([1, 2, 3]))
+    assert np.allclose(counts, np.array([5666, 6552, 52132]))
+
+    # Dropout and decay methods combined
+    mask, masksum = utils.make_adaptive_mask(data, threshold=1, methods=["dropout", "decay"])
+
+    assert mask.shape == masksum.shape == (64350,)
+    assert np.allclose(mask, (masksum >= 1).astype(bool))
+    assert mask.sum() == 50786
+    vals, counts = np.unique(masksum, return_counts=True)
+    assert np.allclose(vals, np.array([0, 1, 2, 3]))
+    assert np.allclose(counts, np.array([13564, 4959, 5349, 40478]))
+
+    # Adding "none" should have no effect
+    mask, masksum = utils.make_adaptive_mask(
+        data, threshold=1, methods=["dropout", "decay", "none"]
+    )
+
+    assert mask.shape == masksum.shape == (64350,)
+    assert np.allclose(mask, (masksum >= 1).astype(bool))
+    assert mask.sum() == 50786
+    vals, counts = np.unique(masksum, return_counts=True)
+    assert np.allclose(vals, np.array([0, 1, 2, 3]))
+    assert np.allclose(counts, np.array([13564, 4959, 5349, 40478]))
+
+    # Just "none"
+    mask, masksum = utils.make_adaptive_mask(data, threshold=1, methods=["none"])
+
+    assert mask.shape == masksum.shape == (64350,)
+    assert np.allclose(mask, (masksum >= 1).astype(bool))
+    assert mask.sum() == 64350
+    vals, counts = np.unique(masksum, return_counts=True)
+    assert np.allclose(vals, np.array([3]))
+    assert np.allclose(counts, np.array([64350]))
+
     # test user-defined mask
     # TODO: Add mask file with no bad voxels to test against
     mask, masksum = utils.make_adaptive_mask(
-        data, mask=pjoin(datadir, "mask.nii.gz"), getsum=True, threshold=3
+        data,
+        mask=pjoin(datadir, "mask.nii.gz"),
+        threshold=3,
+        methods=["dropout", "decay"],
     )
     assert np.allclose(mask, (masksum >= 3).astype(bool))
 
@@ -127,17 +170,17 @@ def test_smoke_make_adaptive_mask():
 
     in the correct format.
 
-    Note: make_adaptive_mask has optional paramters - mask and getsum.
+    Note: make_adaptive_mask has optional paramters - mask and threshold.
     """
     n_samples = 100
     n_echos = 5
     n_times = 20
     data = np.random.random((n_samples, n_echos, n_times))
     mask = np.random.randint(2, size=n_samples)
 
-    assert utils.make_adaptive_mask(data) is not None
-    assert utils.make_adaptive_mask(data, mask=mask) is not None  # functions with mask
-    assert utils.make_adaptive_mask(data, getsum=True) is not None  # functions when getsumis true
+    assert utils.make_adaptive_mask(data, methods=["dropout", "decay"]) is not None
+    # functions with mask
+    assert utils.make_adaptive_mask(data, mask=mask, methods=["dropout", "decay"]) is not None
 
 
 def test_smoke_unmask():

tedana/utils.py

@@ -49,88 +49,159 @@ def reshape_niimg(data):
     return fdata
 
 
-def make_adaptive_mask(data, mask=None, getsum=False, threshold=1):
-    """
-    Make map of `data` specifying longest echo a voxel can be sampled with.
+def make_adaptive_mask(data, mask=None, threshold=1, methods=["dropout"]):
+    """Make map of `data` specifying longest echo a voxel can be sampled with.
 
     Parameters
     ----------
     data : (S x E x T) array_like
-        Multi-echo data array, where `S` is samples, `E` is echos, and `T` is
-        time
+        Multi-echo data array, where `S` is samples, `E` is echos, and `T` is time.
     mask : :obj:`str` or img_like, optional
         Binary mask for voxels to consider in TE Dependent ANAlysis. Default is
         to generate mask from data with good signal across echoes
-    getsum : :obj:`bool`, optional
-        Return `masksum` in addition to `mask`. Default: False
     threshold : :obj:`int`, optional
         Minimum echo count to retain in the mask. Default is 1, which is
         equivalent not thresholding.
+    methods : :obj:`list`, optional
+        List of methods to use for adaptive mask generation. Default is ["dropout"].
+        Valid methods are "decay", "dropout", and "none".
 
     Returns
     -------
     mask : (S,) :obj:`numpy.ndarray`
-        Boolean array of voxels that have sufficient signal in at least one
-        echo
-    masksum : (S,) :obj:`numpy.ndarray`
-        Valued array indicating the number of echos with sufficient signal in a
-        given voxel. Only returned if `getsum = True`
+        Boolean array of voxels that have sufficient signal in at least ``threshold`` echos.
+    adaptive_mask : (S,) :obj:`numpy.ndarray`
+        Valued array indicating the number of echos with sufficient signal in a given voxel.
+
+    Notes
+    -----
+    The adaptive mask can flag "bad" echoes via two methods: dropout and decay.
+    Either or both methods are applied to the mean magnitude across time for each voxel and echo.
+
+    Dropout
+
+    Remove voxels with relatively low mean magnitudes from the mask.
+    This method uses distributions of values across the mask.
+    Therefore, it is sensitive to the quality of the mask.
+    A bad mask may result in a bad adaptive mask.
+
+    This method is implemented as follows:
+
+    a.  Calculate the 33rd percentile of values in the first echo,
+        based on voxel-wise mean over time.
+    b.  Identify the voxel where the first echo's mean value is equal to the 33rd percentile.
+        Basically, this identifies "exemplar" voxel reflecting the 33rd percentile.
+
+        -   The 33rd percentile is arbitrary.
+        -   If more than one voxel has a value exactly equal to the 33rd percentile,
+            keep all of them.
+    c.  For the exemplar voxel from the first echo, calculate 1/3 of the mean value for each echo.
+
+        -   This is the threshold for "good" data.
+        -   The 1/3 value is arbitrary.
+        -   If there was more than one exemplar voxel, retain the the highest value for each echo.
+    d.  For each voxel, count the number of echoes that have a mean value greater than the
+        corresponding echo's threshold.
+
+    Decay
+
+    Determine the echo at which the signal stops decreasing for each voxel.
+    If a voxel's signal stops decreasing as echo time increases, then we can infer that the
+    voxel has either fully dephased (i.e., "bottomed out") or been contaminated by noise.
+    This essentially identifies the last echo with "good" data.
+    For a scan that collects many echoes for T2* estimation or has a relatively short echo
+    spacing, it is possible that a later echo will have a higher value,
+    but the overall trend still shows a decay.
+    This method should not be used in those situations.
+
+    The element-wise minimum value between any selected methods is used to construct the adaptive
+    mask.
     """
     RepLGR.info(
-        "An adaptive mask was then generated, in which each voxel's "
-        "value reflects the number of echoes with 'good' data."
+        f"An adaptive mask was then generated using the {'+'.join(methods)} method(s), "
+        "in which each voxel's value reflects the number of echoes with 'good' data."
     )
-
-    # take temporal mean of echos and extract non-zero values in first echo
-    echo_means = data.mean(axis=-1)  # temporal mean of echos
-    first_echo = echo_means[echo_means[:, 0] != 0, 0]
-
-    # get 33rd %ile of `first_echo` and find corresponding index
-    # NOTE: percentile is arbitrary
-    # TODO: "interpolation" param changed to "method" in numpy 1.22.0
-    #       confirm method="higher" is the same as interpolation="higher"
-    #       Current minimum version for numpy in tedana is 1.16 where
-    #       there is no "method" parameter. Either wait until we bump
-    #       our minimum numpy version to 1.22 or add a version check
-    #       or try/catch statement.
-    perc = np.percentile(first_echo, 33, interpolation="higher")
-    perc_val = echo_means[:, 0] == perc
-
-    # extract values from all echos at relevant index
-    # NOTE: threshold of 1/3 voxel value is arbitrary
-    lthrs = np.squeeze(echo_means[perc_val].T) / 3
-
-    # if multiple samples were extracted per echo, keep the one w/the highest signal
-    if lthrs.ndim > 1:
-        lthrs = lthrs[:, lthrs.sum(axis=0).argmax()]
-
-    # determine samples where absolute value is greater than echo-specific thresholds
-    # and count # of echos that pass criterion
-    masksum = (np.abs(echo_means) > lthrs).sum(axis=-1)
+    assert methods, "No methods provided for adaptive mask generation."
+    assert all([method.lower() in ["decay", "dropout", "none"] for method in methods])
+
+    n_samples, n_echos, _ = data.shape
+    adaptive_masks = []
+
+    # Generate a base adaptive mask that flags any NaNs or negative values
+    base_adaptive_mask = np.full(n_samples, n_echos, dtype=int)
+    for i_voxel in range(n_samples):
+        voxel_data = data[i_voxel, :, :]
+        nonnan_echoes = ~np.any(np.isnan(voxel_data), axis=1)
+        nonneg_echoes = ~np.any(voxel_data < 0, axis=1)
+        good_echoes = nonnan_echoes * nonneg_echoes
+        # Find the index of the last True element in a 1D boolean array
+        last_good_echo = (np.where(good_echoes)[0][-1] + 1) if np.any(good_echoes) else 0
+        base_adaptive_mask[i_voxel] = last_good_echo
+
+    adaptive_masks.append(base_adaptive_mask)
+
+    if ("dropout" in methods) or ("decay" in methods):
+        echo_means = data.mean(axis=-1)  # temporal mean of echos
+
+    if "dropout" in methods:
+        # take temporal mean of echos and extract non-zero values in first echo
+        first_echo = echo_means[echo_means[:, 0] != 0, 0]
+
+        # get 33rd %ile of `first_echo` and find corresponding index
+        # NOTE: percentile is arbitrary
+        # TODO: "interpolation" param changed to "method" in numpy 1.22.0
+        #       confirm method="higher" is the same as interpolation="higher"
+        #       Current minimum version for numpy in tedana is 1.16 where
+        #       there is no "method" parameter. Either wait until we bump
+        #       our minimum numpy version to 1.22 or add a version check
+        #       or try/catch statement.
+        perc = np.percentile(first_echo, 33, interpolation="higher")
+        perc_val = echo_means[:, 0] == perc
+
+        # extract values from all echos at relevant index
+        # NOTE: threshold of 1/3 voxel value is arbitrary
+        lthrs = np.squeeze(echo_means[perc_val].T) / 3
+
+        # if multiple samples were extracted per echo, keep the one w/the highest signal
+        if lthrs.ndim > 1:
+            lthrs = lthrs[:, lthrs.sum(axis=0).argmax()]
+
+        # determine samples where absolute value is greater than echo-specific thresholds
+        # and count # of echos that pass criterion
+        dropout_adaptive_mask = (np.abs(echo_means) > lthrs).sum(axis=-1)
+        adaptive_masks.append(dropout_adaptive_mask)
+
+    if "decay" in methods:
+        # Determine where voxels stop decreasing in signal from echo to echo
+        echo_diffs = np.hstack((np.full((n_samples, 1), -1), np.diff(echo_means, axis=1)))
+        diff_mask = echo_diffs >= 0  # flag where signal is not decreasing
+        last_decreasing_echo = diff_mask.argmax(axis=1)
+        last_decreasing_echo[last_decreasing_echo == 0] = n_echos  # if no increase, set to n_echos
+        adaptive_masks.append(last_decreasing_echo)
+
+    # Retain the most conservative of the selected adaptive mask estimates
+    adaptive_mask = np.minimum.reduce(adaptive_masks)
 
     if mask is None:
         # make it a boolean mask to (where we have at least `threshold` echoes with good signal)
-        mask = (masksum >= threshold).astype(bool)
-        masksum[masksum < threshold] = 0
+        mask = (adaptive_mask >= threshold).astype(bool)
+        adaptive_mask[adaptive_mask < threshold] = 0
     else:
         # if the user has supplied a binary mask
         mask = reshape_niimg(mask).astype(bool)
-        masksum = masksum * mask
-        # reduce mask based on masksum
+        adaptive_mask = adaptive_mask * mask
+        # reduce mask based on adaptive_mask
         # TODO: Use visual report to make checking the reduced mask easier
-        if np.any(masksum[mask] < threshold):
-            n_bad_voxels = np.sum(masksum[mask] < threshold)
+        if np.any(adaptive_mask[mask] < threshold):
+            n_bad_voxels = np.sum(adaptive_mask[mask] < threshold)
             LGR.warning(
                 f"{n_bad_voxels} voxels in user-defined mask do not have good "
                 "signal. Removing voxels from mask."
             )
-            masksum[masksum < threshold] = 0
-            mask = masksum.astype(bool)
-
-    if getsum:
-        return mask, masksum
+            adaptive_mask[adaptive_mask < threshold] = 0
+            mask = adaptive_mask.astype(bool)
 
-    return mask
+    return mask, adaptive_mask
 
 
 def unmask(data, mask):

tedana/workflows/t2smap.py

@@ -84,6 +84,16 @@ def _get_parser():
         help=("Filenaming convention. bids will use the latest BIDS derivatives version."),
         default="bids",
     )
+    optional.add_argument(
+        "--masktype",
+        dest="masktype",
+        required=False,
+        action="store",
+        nargs="+",
+        help="Method(s) by which to define the adaptive mask.",
+        choices=["dropout", "decay", "none"],
+        default=["dropout"],
+    )
     optional.add_argument(
         "--fittype",
         dest="fittype",
@@ -152,6 +162,7 @@ def t2smap_workflow(
     mask=None,
     prefix="",
     convention="bids",
+    masktype=["dropout"],
     fittype="loglin",
     fitmode="all",
     combmode="t2s",
@@ -176,6 +187,8 @@ def t2smap_workflow(
     mask : :obj:`str`, optional
         Binary mask of voxels to include in TE Dependent ANAlysis. Must be spatially
         aligned with `data`.
+    masktype : {'dropout', 'decay'} or :obj:`list`, optional
+        Method(s) by which to define the adaptive mask. Default is ["dropout"].
     fittype : {'loglin', 'curvefit'}, optional
         Monoexponential fitting method.
         'loglin' means to use the the default linear fit to the log of
@@ -278,7 +291,12 @@ def t2smap_workflow(
         LGR.info("Computing adaptive mask")
     else:
         LGR.info("Using user-defined mask")
-    mask, masksum = utils.make_adaptive_mask(catd, mask=mask, getsum=True, threshold=1)
+    mask, masksum = utils.make_adaptive_mask(
+        catd,
+        mask=mask,
+        threshold=1,
+        methods=masktype,
+    )
 
     LGR.info("Computing adaptive T2* map")
     if fitmode == "all":