From 9b818d5da99486229903981e6f7f290102e7c850 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Wed, 22 Jul 2015 09:20:03 +0100
Subject: [PATCH] Standard space cluster results have different column names,
and the coordinates are in standard space, rather than voxels. Fixed the
former, but not the latter.
---
fsl/data/featresults.py | 38 +++++++++++++++++++++++++++++++++++---
1 file changed, 35 insertions(+), 3 deletions(-)
diff --git a/fsl/data/featresults.py b/fsl/data/featresults.py
index e34fc8489..9901e55e5 100644
--- a/fsl/data/featresults.py
+++ b/fsl/data/featresults.py
@@ -215,16 +215,34 @@ def loadClusterResults(featdir, settings, contrast):
'Z-COG X (vox)' : ('zcogx', float),
'Z-COG Y (vox)' : ('zcogy', float),
'Z-COG Z (vox)' : ('zcogz', float),
+ 'Z-MAX X (mm)' : ('zmaxx', int),
+ 'Z-MAX Y (mm)' : ('zmaxy', int),
+ 'Z-MAX Z (mm)' : ('zmaxz', int),
+ 'Z-COG X (mm)' : ('zcogx', float),
+ 'Z-COG Y (mm)' : ('zcogy', float),
+ 'Z-COG Z (mm)' : ('zcogz', float),
'COPE-MAX' : ('copemax', float),
'COPE-MAX X (vox)' : ('copemaxx', int),
'COPE-MAX Y (vox)' : ('copemaxy', int),
- 'COPE-MAX Z (vox)' : ('copemaxz', int),
+ 'COPE-MAX Z (vox)' : ('copemaxz', int),
+ 'COPE-MAX X (mm)' : ('copemaxx', int),
+ 'COPE-MAX Y (mm)' : ('copemaxy', int),
+ 'COPE-MAX Z (mm)' : ('copemaxz', int),
'COPE-MEAN' : ('copemean', float)}
# The cluster.txt file is converted
# into a list of Cluster objects,
# each of which encapsulates
# information about one cluster.
+ #
+ # TODO The coordinates (e.g. 'ZMAX X (mm)')
+ # for standard space results (in e.g.
+ # 'cluster_zstatX_std.txt') are in MNI152
+ # space coordinates, and need to be
+ # transformed into voxel coordinates. Or a
+ # flag needs to be set on the Cluster object
+ # so users know that the coordinates are in
+ # standard space.
class Cluster(object):
def __init__(self, **kwargs):
for name, val in kwargs.items():
@@ -235,10 +253,24 @@ def loadClusterResults(featdir, settings, contrast):
setattr(self, attrName, val)
- clusterFile = op.join(featdir, 'cluster_zstat{}.txt'.format(contrast + 1))
+ # Cluster files are named like
+ # 'cluster_zstatX.txt', where
+ # X is the COPE number
+ clusterFile = op.join(
+ featdir, 'cluster_zstat{}.txt'.format(contrast + 1))
if not op.exists(clusterFile):
- return None
+
+ # If the analysis was performed in standard
+ # space (e.g. a higher level group analysis),
+ # the cluster file will instead be called
+ # cluster_zstatX_std.txt', so we'd better
+ # check for that too.
+ clusterFile = op.join(
+ featdir, 'cluster_zstat{}_std.txt'.format(contrast + 1))
+
+ if not op.exists(clusterFile):
+ return None
log.debug('Loading cluster results for contrast {} from {}'.format(
contrast, clusterFile))
--
GitLab