def measure_ttest_fsl (mean1fname, mean2fname,\
var1fname, var2fname, \
std1fname, std2fname, \
numsubjs1, numsubjs2, \
experimentname, outdir, exclude_idx=-1):
if not os.path.exists (outdir):
os.mkdir (outdir)
olddir = os.getcwd()
os.chdir (outdir)
#following the equation:
#t = (m1 - m2) / sqrt( (v1^2)/N1 + (v2^2)/N2 )
#from:
#http://en.wikipedia.org/wiki/Student%27s_t-test#Unequal_sample_sizes.2C_unequal_variance
num1fname = outdir + os.path.sep + experimentname + '_ttest_num1'
den1fname = outdir + os.path.sep + experimentname + '_ttest_den1'
den2fname = outdir + os.path.sep + experimentname + '_ttest_den2'
denfname = outdir + os.path.sep + experimentname + '_ttest_denom'
ttstfname = outdir + os.path.sep + experimentname + '_ttest'
au.fslmaths (mean1fname + ' -sub ' + mean2fname + ' ' + num1fname)
au.fslmaths (var1fname + ' -sqr -div ' + str(numsubjs1) + ' ' + den1fname)
au.fslmaths (var2fname + ' -sqr -div ' + str(numsubjs2) + ' ' + den2fname)
au.fslmaths (den1fname + ' -add ' + den2fname + ' -sqrt ' + denfname )
au.fslmaths (num1fname + ' -div ' + denfname + ' ' + ttstfname)
# imrm (num1fname)
# imrm (den1fname)
# imrm (den2fname)
# imrm (denfname)
os.chdir(olddir)
return ttstfname
def measure_bhattacharyya_distance_fsl (mean1fname, mean2fname, \
var1fname, var2fname, \
std1fname, std2fname, \
numsubjs1, numsubjs2, \
experimentname, outdir, exclude_idx=-1):
if not os.path.exists(outdir):
os.mkdir(outdir)
olddir = os.getcwd()
os.chdir(outdir)
#following the equations:
#1/4 * ((m1-m2)^2/(var1+var2)) + 1/2 * (log( (var1+var2)/(2*std1*std2) ))
#from:
#1
#Bhattacharyya clustering with applications to mixture simplifications
#Frank Nielsen, Sylvain Boltz, and Olivier Schwander
#2010 International Conference on Pattern Recognition
#2
#The Divergence and Bhattacharyya Distance Measures in Signal Selection
#Kailath, T.
#http://dx.doi.org/10.1109/TCOM.1967.1089532
num1fname = outdir + os.path.sep + experimentname + '_bhatta_num1'
den1fname = outdir + os.path.sep + experimentname + '_bhatta_denom1'
bhatta1 = outdir + os.path.sep + experimentname + '_bhatta_first'
au.fslmaths(mean1fname + ' -sub ' + mean2fname + ' -sqr ' + num1fname)
au.fslmaths(var1fname + ' -add ' + var2fname + ' ' + den1fname)
au.fslmaths(num1fname + ' -div ' + den1fname + ' -div 4 ' + bhatta1)
num2fname = outdir + os.path.sep + experimentname + '_bhatta_num2'
au.fslmaths(var1fname + ' -add ' + var2fname + ' ' + num2fname)
den2fname = outdir + os.path.sep + experimentname + '_bhatta_denom2'
bhatta2 = outdir + os.path.sep + experimentname + '_bhatta_secnd'
au.fslmaths(std1fname + ' -mul ' + std2fname + ' -mul 2 ' + den2fname)
au.fslmaths(num2fname + ' -div ' + den2fname + ' -log -div 2 ' + bhatta2)
bhatta = outdir + os.path.sep + experimentname + '_' + au.bhattacharyya_str(
)
au.fslmaths(bhatta1 + ' -add ' + bhatta2 + ' ' + bhatta)
# au.imrm (num1fname)
# au.imrm (den1fname)
# au.imrm (bhatta1)
# au.imrm (num2fname)
# au.imrm (den2fname)
# au.imrm (bhatta2)
os.chdir(olddir)
return bhatta
def measure_bhattacharyya_distance_fsl (mean1fname, mean2fname, \
var1fname, var2fname, \
std1fname, std2fname, \
numsubjs1, numsubjs2, \
experimentname, outdir, exclude_idx=-1):
if not os.path.exists (outdir):
os.mkdir (outdir)
olddir = os.getcwd()
os.chdir (outdir)
#following the equations:
#1/4 * ((m1-m2)^2/(var1+var2)) + 1/2 * (log( (var1+var2)/(2*std1*std2) ))
#from:
#1
#Bhattacharyya clustering with applications to mixture simplifications
#Frank Nielsen, Sylvain Boltz, and Olivier Schwander
#2010 International Conference on Pattern Recognition
#2
#The Divergence and Bhattacharyya Distance Measures in Signal Selection
#Kailath, T.
#http://dx.doi.org/10.1109/TCOM.1967.1089532
num1fname = outdir + os.path.sep + experimentname + '_bhatta_num1'
den1fname = outdir + os.path.sep + experimentname + '_bhatta_denom1'
bhatta1 = outdir + os.path.sep + experimentname + '_bhatta_first'
au.fslmaths (mean1fname + ' -sub ' + mean2fname + ' -sqr ' + num1fname)
au.fslmaths (var1fname + ' -add ' + var2fname + ' ' + den1fname)
au.fslmaths (num1fname + ' -div ' + den1fname + ' -div 4 ' + bhatta1)
num2fname = outdir + os.path.sep + experimentname + '_bhatta_num2'
au.fslmaths (var1fname + ' -add ' + var2fname + ' ' + num2fname)
den2fname = outdir + os.path.sep + experimentname + '_bhatta_denom2'
bhatta2 = outdir + os.path.sep + experimentname + '_bhatta_secnd'
au.fslmaths (std1fname + ' -mul ' + std2fname + ' -mul 2 ' + den2fname)
au.fslmaths (num2fname + ' -div ' + den2fname + ' -log -div 2 ' + bhatta2)
bhatta = outdir + os.path.sep + experimentname + '_' + au.bhattacharyya_str()
au.fslmaths (bhatta1 + ' -add ' + bhatta2 + ' ' + bhatta)
# au.imrm (num1fname)
# au.imrm (den1fname)
# au.imrm (bhatta1)
# au.imrm (num2fname)
# au.imrm (den2fname)
# au.imrm (bhatta2)
os.chdir(olddir)
return bhatta