else:
data_min = data[data.nonzero()].min()
return [data_min, data_max]
print 'getting range'
ranges = np.array([get_range(pfile) for pfile in pfiles])
dmin = ranges.min()
dmax = ranges.max()
print 'min=%.4f; max=%.4f' % (dmin, dmax)
###
###
# Surface Viz
for i, pfile in enumerate(pfiles):
print pfile
oprefix = path.join(odir,
"C4_fstats_global_easythresh_surface_scan%i" % (i + 1))
sw = SurfWrap(name=factor,
infile=pfile,
cbar="red-yellow",
outprefix=oprefix)
sw.min = dmin
sw.max = dmax
sw.run(compilation="box")
sw.montage(compilation="stick")
###
# Overlap
overlap_lh = scan1_lh[:] * scan2_lh[:]
overlap_rh = scan1_rh[:] * scan2_rh[:]
###
###
# Plot overlap
import code
sw0 = SurfWrap()
sw0.set_underlay()
sw0.set_options()
sw0.min = 0
sw0.max = 2
sw0.sign = "pos"
oprefix = path.join(odir, "E_global_easythresh_surface_overlap")
sw0.set_output(oprefix)
scan1_surfs = {"lh": scan1_lh, "rh": scan1_rh}
scan2_surfs = {"lh": scan2_lh, "rh": scan2_rh}
overlap_surfs = {"lh": overlap_lh, "rh": overlap_rh}
#code.interact(local=locals())
for hemi in sw0.hemis:
print "visualize %s" % hemi
# Bring up the beauty (the underlay)
data = img.get_data()
data_max = data.max()
if data_max == 0:
data_min = data_max
else:
data_min = data[data.nonzero()].min()
return [data_min, data_max]
print 'getting range'
ranges = np.array([ get_range(pfile) for pfile in pfiles ])
dmin = ranges.min()
dmax = ranges.max()
print 'min=%.4f; max=%.4f' % (dmin,dmax)
###
###
# Surface Viz
for i,pfile in enumerate(pfiles):
print pfile
oprefix = path.join(odir, "C4_fstats_global_easythresh_surface_scan%i" % (i+1))
sw = SurfWrap(name=factor, infile=pfile, cbar="red-yellow",
outprefix=oprefix)
sw.min = dmin; sw.max = dmax
sw.run(compilation="box")
sw.montage(compilation="stick")
###
data_max = data.max()
if data_max == 0:
data_min = data_max
else:
data_min = data[data.nonzero()].min()
return [data_min, data_max]
print "getting range"
ranges = np.array([get_range(pfile) for pfile in pfiles])
dmin = ranges[ranges != 0].min()
dmax = ranges[ranges != 0].max()
print "min=%.4f; max=%.4f" % (dmin, dmax)
###
###
# Surface Viz
for i, pfile in enumerate(pfiles):
print pfile
oprefix = path.join(odir, "C2_global_perms_surface_scan%i" % (i + 1))
sw = SurfWrap(name=factor, infile=pfile, cbar="red-yellow", outprefix=oprefix)
sw.min = dmin
sw.max = dmax
sw.run(compilation="box")
sw.montage(compilation="stick")
###
data = img.get_data()
data_max = data.max()
if data_max == 0:
data_min = data_max
else:
data_min = data[data.nonzero()].min()
return [data_min, data_max]
print 'getting range'
ranges = np.array([ get_range(pfile) for pfile in pfiles ])
dmin = ranges[ranges!=0].min()
dmax = ranges[ranges!=0].max()
print 'min=%.4f; max=%.4f' % (dmin,dmax)
###
###
# Surface Viz
for i,pfile in enumerate(pfiles):
print pfile
oprefix = path.join(odir, "B_global_perms_surface_scan%i" % (i+1))
sw = SurfWrap(name=factor, infile=pfile, cbar="red-yellow",
outprefix=oprefix)
sw.min = dmin; sw.max = dmax
sw.run(compilation="box")
sw.montage(compilation="stick")
###
scan2_lh[scan2_lh>dmin] = 2
scan2_rh[scan2_rh>dmin] = 2
# Overlap
overlap_lh = scan1_lh[:] * scan2_lh[:]
overlap_rh = scan1_rh[:] * scan2_rh[:]
###
###
# Plot overlap
sw0 = SurfWrap()
sw0.set_underlay()
sw0.set_options()
sw0.min = 1; sw0.max = 2; sw0.sign = "pos"
oprefix = path.join(odir, "D_perms_surface_overlap")
sw0.set_output(oprefix)
scan1_surfs = {"lh": scan1_lh, "rh": scan1_rh}
scan2_surfs = {"lh": scan2_lh, "rh": scan2_rh}
overlap_surfs = {"lh": overlap_lh, "rh": overlap_rh}
for hemi in sw0.hemis:
print "visualize %s" % hemi
# Bring up the beauty (the underlay)
brain = Brain(sw0.subject_id, hemi, sw0.surf, \
config_opts=sw0.config_opts, \
subjects_dir=sw0.subjects_dir)
from os import path
from surfwrap import SurfWrap
obase = "/home2/data/Projects/CWAS/adhd200_rerun/cwas"
comparisons = ["adhdc_vs_adhdi", "tdc_vs_adhdc", "tdc_vs_adhdi"]
# GLOBAL!
preproc = "global"
for comparison in comparisons:
print "group comparison: %s" % comparison
# Input pfile
distdir = path.join(obase, "%s_rois_random_k3200" % preproc)
mdmrdir = path.join(distdir, "%s_gender+age+iq+mean_FD.mdmr" % comparison)
pfile = path.join(mdmrdir, "log_pvals_%s.nii.gz" % comparison)
# Output oprefix
odir = path.join(mdmrdir, "images")
if not path.exists(odir): os.mkdir(odir)
oprefix = path.join(odir, path.basename(pfile).replace(".nii.gz", ""))
# Surface Viz
sw = SurfWrap(name=comparison, infile=pfile, cbar="red-yellow", outprefix=oprefix)
sw.min = 1.3
sw.run()
# import pysurfer
# pysurfer = reload(pysurfer)
# SurfWrap = pysurfer.SurfWrap
# Overlap top 15% between mdmr and glm
lh_overlap = (lh_cwas_perc>0)*1 + (lh_glm_perc>0)*2
rh_overlap = (rh_cwas_perc>0)*1 + (rh_glm_perc>0)*2
###
###
# Plot top percentiles
print "plot percentiles"
sw0 = SurfWrap(hemis=['lh'])
sw0.set_underlay()
sw0.set_options()
sw0.min = 1; sw0.max = 3; sw0.sign = "pos"
oprefix = op.join(figdir, "B_surface_percentiles")
sw0.set_output(oprefix)
cwas_perc_surfs = {"lh": lh_cwas_perc}
glm_perc_surfs = {"lh": lh_glm_perc}
overlap_surfs = {"lh": lh_overlap}
for hemi in sw0.hemis:
print "visualize %s" % hemi
## MDMR
#oprefix = op.join(figdir, "B_%s_percentiles_mdmr" % scans[i])
#sw0.set_output(oprefix)
#
#brain = Brain(sw0.subject_id, hemi, sw0.surf, \
# Overlap top 15% between mdmr and glm
lh_overlap = (lh_cwas_perc > 0) * 1 + (lh_glm_perc > 0) * 2
rh_overlap = (rh_cwas_perc > 0) * 1 + (rh_glm_perc > 0) * 2
###
###
# Plot top percentiles
print "plot percentiles"
sw0 = SurfWrap(hemis=['lh'])
sw0.set_underlay()
sw0.set_options()
sw0.min = 1
sw0.max = 3
sw0.sign = "pos"
oprefix = op.join(figdir, "B_surface_percentiles")
sw0.set_output(oprefix)
cwas_perc_surfs = {"lh": lh_cwas_perc}
glm_perc_surfs = {"lh": lh_glm_perc}
overlap_surfs = {"lh": lh_overlap}
for hemi in sw0.hemis:
print "visualize %s" % hemi
## MDMR
#oprefix = op.join(figdir, "B_%s_percentiles_mdmr" % scans[i])
#sw0.set_output(oprefix)
obase = "/home2/data/Projects/CWAS/adhd200_rerun/cwas"
comparisons = ["adhdc_vs_adhdi", "tdc_vs_adhdc", "tdc_vs_adhdi"]
# GLOBAL!
preproc = "global"
for comparison in comparisons:
print "group comparison: %s" % comparison
# Input pfile
distdir = path.join(obase, "%s_rois_random_k3200" % preproc)
mdmrdir = path.join(distdir, "%s_gender+age+iq+mean_FD.mdmr" % comparison)
pfile = path.join(mdmrdir, "log_pvals_%s.nii.gz" % comparison)
# Output oprefix
odir = path.join(mdmrdir, "images")
if not path.exists(odir): os.mkdir(odir)
oprefix = path.join(odir, path.basename(pfile).replace(".nii.gz", ""))
# Surface Viz
sw = SurfWrap(name=comparison,
infile=pfile,
cbar="red-yellow",
outprefix=oprefix)
sw.min = 1.3
sw.run()
# import pysurfer
# pysurfer = reload(pysurfer)
# SurfWrap = pysurfer.SurfWrap
# Overlap
overlap_lh = scan1_lh[:] * scan2_lh[:]
overlap_rh = scan1_rh[:] * scan2_rh[:]
###
###
# Plot overlap
import code
sw0 = SurfWrap()
sw0.set_underlay()
sw0.set_options()
sw0.min = 0
sw0.max = 2
sw0.sign = "pos"
oprefix = path.join(odir, "E_global_easythresh_surface_overlap")
sw0.set_output(oprefix)
scan1_surfs = {"lh": scan1_lh, "rh": scan1_rh}
scan2_surfs = {"lh": scan2_lh, "rh": scan2_rh}
overlap_surfs = {"lh": overlap_lh, "rh": overlap_rh}
# code.interact(local=locals())
for hemi in sw0.hemis:
print "visualize %s" % hemi
# Bring up the beauty (the underlay)