diff --git a/fsl/data/featanalysis.py b/fsl/data/featanalysis.py
index 320653c143ef5eb2afbec060a089ca282e509b2b..93dba289633ad11e8bef434d82671dccf97851eb 100644
--- a/fsl/data/featanalysis.py
+++ b/fsl/data/featanalysis.py
@@ -43,6 +43,7 @@ The following functions return the names of various files of interest:
getZStatFile
getZFStatFile
getClusterMaskFile
+ getFClusterMaskFile
"""
@@ -328,19 +329,22 @@ def isFirstLevelAnalysis(settings):
return settings['level'] == '1'
-def loadClusterResults(featdir, settings, contrast):
+def loadClusterResults(featdir, settings, contrast, ftest=False):
"""If cluster thresholding was used in the FEAT analysis, this function
will load and return the cluster results for the specified (0-indexed)
- contrast number.
+ contrast or f-test.
- If there are no cluster results for the given contrast, ``None`` is
- returned.
+ If there are no cluster results for the given contrast/f-test, ``None``
+ is returned.
An error will be raised if the cluster file cannot be parsed.
:arg featdir: A FEAT directory.
:arg settings: A FEAT settings dictionary.
- :arg contrast: 0-indexed contrast number.
+ :arg contrast: 0-indexed contrast or f-test number.
+ :arg ftest: If ``False`` (default), return cluster results for
+ the contrast numbered ``contrast``. Otherwise, return
+ cluster results for the f-test numbered ``contrast``.
:returns: A list of ``Cluster`` instances, each of which contains
information about one cluster. A ``Cluster`` object has the
@@ -361,11 +365,16 @@ def loadClusterResults(featdir, settings, contrast):
gravity.
``zcogz`` Z voxel coordinate of cluster centre of
gravity.
- ``copemax`` Maximum COPE value in cluster.
- ``copemaxx`` X voxel coordinate of maximum COPE value.
+ ``copemax`` Maximum COPE value in cluster (not
+ present for f-tests).
+ ``copemaxx`` X voxel coordinate of maximum COPE value
+ (not present for f-tests).
``copemaxy`` Y voxel coordinate of maximum COPE value.
+ (not present for f-tests).
``copemaxz`` Z voxel coordinate of maximum COPE value.
+ (not present for f-tests).
``copemean`` Mean COPE of all voxels in the cluster.
+ (not present for f-tests).
============ =========================================
"""
@@ -375,7 +384,11 @@ def loadClusterResults(featdir, settings, contrast):
# the ZMax/COG etc coordinates
# are usually in voxel coordinates
coordXform = np.eye(4)
- clusterFile = op.join(featdir, f'cluster_zstat{contrast + 1}.txt')
+
+ if ftest: prefix = 'cluster_zfstat'
+ else: prefix = 'cluster_zstat'
+
+ clusterFile = op.join(featdir, f'{prefix}{contrast + 1}.txt')
if not op.exists(clusterFile):
@@ -384,7 +397,7 @@ def loadClusterResults(featdir, settings, contrast):
# the cluster file will instead be called
# 'cluster_zstatX_std.txt', so we'd better
# check for that too.
- clusterFile = op.join(featdir, f'cluster_zstat{contrast + 1}_std.txt')
+ clusterFile = op.join(featdir, f'{prefix}{contrast + 1}_std.txt')
if not op.exists(clusterFile):
return None
@@ -395,9 +408,6 @@ def loadClusterResults(featdir, settings, contrast):
# later on.
coordXform = fslimage.Image(getDataFile(featdir)).worldToVoxMat
- log.debug('Loading cluster results for contrast %s from %s',
- contrast, clusterFile)
-
# The cluster.txt file is converted
# into a list of Cluster objects,
# each of which encapsulates
@@ -414,10 +424,17 @@ def loadClusterResults(featdir, settings, contrast):
# if cluster thresholding was not used,
# the cluster table will not contain
- # P valuse.
+ # P values.
if not hasattr(self, 'p'): self.p = 1.0
if not hasattr(self, 'logp'): self.logp = 0.0
+ # F-test cluster results will not have
+ # COPE-* results
+ if not hasattr(self, 'copemaxx'): self.copemaxx = np.nan
+ if not hasattr(self, 'copemaxy'): self.copemaxy = np.nan
+ if not hasattr(self, 'copemaxz'): self.copemaxz = np.nan
+ if not hasattr(self, 'copemean'): self.copemean = np.nan
+
# This dict provides a mapping between
# Cluster object attribute names, and
# the corresponding column name in the
@@ -449,10 +466,9 @@ def loadClusterResults(featdir, settings, contrast):
'COPE-MAX Z (mm)' : 'copemaxz',
'COPE-MEAN' : 'copemean'}
- # An error will be raised if the
- # cluster file does not exist (e.g.
- # if the specified contrast index
- # is invalid)
+ log.debug('Loading cluster results for contrast %s from %s',
+ contrast, clusterFile)
+
with open(clusterFile, 'rt') as f:
# Get every line in the file,
@@ -474,12 +490,11 @@ def loadClusterResults(featdir, settings, contrast):
colNames = colNames.split('\t')
clusterLines = [cl .split('\t') for cl in clusterLines]
- # Turn each cluster line into a
- # Cluster instance. An error will
- # be raised if the columm names
- # are unrecognised (i.e. not in
- # the colmap above), or if the
- # file is poorly formed.
+ # Turn each cluster line into a Cluster
+ # instance. An error will be raised if the
+ # columm names are unrecognised (i.e. not
+ # in the colmap above), or if the file is
+ # poorly formed.
clusters = [Cluster(**dict(zip(colNames, cl))) for cl in clusterLines]
# Make sure all coordinates are in voxels -
@@ -627,3 +642,15 @@ def getClusterMaskFile(featdir, contrast):
"""
mfile = op.join(featdir, f'cluster_mask_zstat{contrast + 1}')
return fslimage.addExt(mfile, mustExist=True)
+
+
+def getFClusterMaskFile(featdir, ftest):
+ """Returns the path of the cluster mask file for the specified f-test.
+
+ Raises a :exc:`~fsl.utils.path.PathError` if the file does not exist.
+
+ :arg featdir: A FEAT directory.
+ :arg contrast: The f-test number (0-indexed).
+ """
+ mfile = op.join(featdir, f'cluster_mask_zfstat{ftest + 1}')
+ return fslimage.addExt(mfile, mustExist=True)