Update runEddy script to work with new multi-threaded version.

The eddy_cpu command is called twice - once with --nthr=1, and again with --nthr=8

Note that these changes will not work with the openmp eddy build, so do not merge / use this MR until threddy has been released.

fsl_course/feat3/feedsRun5.py

@@ -24,6 +24,13 @@ newFSF = op.join(outDir, "design.fsf")
 cmd = "./cleanFSF.py {0} {1} {2} {3} {4} {5}".format(origFSF, newFSF, origDataDir, dataDir, outDir, origFSLDir)
 utils.run(cmd)
 
+# For conda version, default_flobs.flobs is in new location
+
+with open(newFSF, 'rt') as f:
+    contents = f.read()
+with open(newFSF, 'wt') as f:
+    f.write(contents.replace('/etc/', '/data/feat5/'))
+
 # run FEAT
 utils.run("unset SGE_ROOT; feat {0}".format(op.join(outDir, "design.fsf")))