region labelling and code cleanup

harvardoxford_cortical_labels.csv

@@ -0,0 +1,48 @@
+1,Frontal Pole
+2,Insular Cortex
+3,Superior Frontal Gyrus
+4,Middle Frontal Gyrus
+5,Inferior Frontal Gyrus; pars triangularis
+6,Inferior Frontal Gyrus; pars opercularis
+7,Precentral Gyrus
+8,Temporal Pole
+9,Superior Temporal Gyrus; anterior division
+10,Superior Temporal Gyrus; posterior division
+11,Middle Temporal Gyrus; anterior division
+12,Middle Temporal Gyrus; posterior division
+13,Middle Temporal Gyrus; temporooccipital part
+14,Inferior Temporal Gyrus; anterior division
+15,Inferior Temporal Gyrus; posterior division
+16,Inferior Temporal Gyrus; temporooccipital part
+17,Postcentral Gyrus
+18,Superior Parietal Lobule
+19,Supramarginal Gyrus; anterior division
+20,Supramarginal Gyrus; posterior division
+21,Angular Gyrus
+22,Lateral Occipital Cortex; superior division
+23,Lateral Occipital Cortex; inferior division
+24,Intracalcarine Cortex
+25,Frontal Medial Cortex
+26,Juxtapositional Lobule Cortex (formerly Supplementary Motor Cortex)
+27,Subcallosal Cortex
+28,Paracingulate Gyrus
+29,Cingulate Gyrus; anterior division
+30,Cingulate Gyrus; posterior division
+31,Precuneous Cortex
+32,Cuneal Cortex
+33,Frontal Orbital Cortex
+34,Parahippocampal Gyrus; anterior division
+35,Parahippocampal Gyrus; posterior division
+36,Lingual Gyrus
+37,Temporal Fusiform Cortex; anterior division
+38,Temporal Fusiform Cortex; posterior division
+39,Temporal Occipital Fusiform Cortex
+40,Occipital Fusiform Gyrus
+41,Frontal Operculum Cortex
+42,Central Opercular Cortex
+43,Parietal Operculum Cortex
+44,Planum Polare
+45,Heschl's Gyrus (includes H1 and H2)
+46,Planum Temporale
+47,Supracalcarine Cortex
+48,Occipital Pole

harvardoxford_subcortical_labels.csv

@@ -0,0 +1,21 @@
+2,Left Cerebral White Matter
+3,Left Cerebral Cortex 
+4,Left Lateral Ventrical
+10,Left Thalamus
+11,Left Caudate
+12,Left Putamen
+13,Left Pallidum
+16,Brain-Stem
+17,Left Hippocampus
+18,Left Amygdala
+26,Left Accumbens
+41,Right Cerebral White Matter
+42,Right Cerebral Cortex 
+43,Right Lateral Ventricle
+49,Right Thalamus
+50,Right Caudate
+51,Right Putamen
+52,Right Pallidum
+53,Right Hippocampus
+54,Right Amygdala
+58,Right Accumbens

juelich_labels.csv

@@ -0,0 +1,121 @@
+1,GM Anterior intra-parietal sulcus hIP1 L
+2,GM Anterior intra-parietal sulcus hIP1 R
+3,GM Anterior intra-parietal sulcus hIP2 L
+4,GM Anterior intra-parietal sulcus hIP2 R
+5,GM Anterior intra-parietal sulcus hIP3 L
+6,GM Anterior intra-parietal sulcus hIP3 R
+7,GM Amygdala_centromedial group L
+8,GM Amygdala_centromedial group R
+9,GM Amygdala_laterobasal group L
+10,GM Amygdala_laterobasal group R
+11,GM Amygdala_superficial group L
+12,GM Amygdala_superficial group R
+13,GM Broca's area BA44 L
+14,GM Broca's area BA44 R
+15,GM Broca's area BA45 L
+16,GM Broca's area BA45 R
+17,GM Hippocampus cornu ammonis L
+18,GM Hippocampus cornu ammonis R
+19,GM Hippocampus entorhinal cortex L
+20,GM Hippocampus entorhinal cortex R
+21,GM Hippocampus dentate gyrus L
+22,GM Hippocampus dentate gyrus R
+23,GM Hippocampus hippocampal-amygdaloid transition area L
+24,GM Hippocampus hippocampal-amygdaloid transition area R
+25,GM Hippocampus subiculum L
+26,GM Hippocampus subiculum R
+27,GM Inferior parietal lobule PF L
+28,GM Inferior parietal lobule PF R
+29,GM Inferior parietal lobule PFcm L
+30,GM Inferior parietal lobule PFcm R
+31,GM Inferior parietal lobule PFm L
+32,GM Inferior parietal lobule PFm R
+33,GM Inferior parietal lobule PFop L
+34,GM Inferior parietal lobule PFop R
+35,GM Inferior parietal lobule PFt L
+36,GM Inferior parietal lobule PFt R
+37,GM Inferior parietal lobule Pga L
+38,GM Inferior parietal lobule Pga R
+39,GM Inferior parietal lobule PGp L
+40,GM Inferior parietal lobule PGp R
+41,GM Primary auditory cortex TE1.0 L
+42,GM Primary auditory cortex TE1.0 R
+43,GM Primary auditory cortex TE1.1 L
+44,GM Primary auditory cortex TE1.1 R
+45,GM Primary auditory cortex TE1.2 L
+46,GM Primary auditory cortex TE1.2 R
+47,GM Primary motor cortex BA4a L
+48,GM Primary motor cortex BA4a R
+49,GM Primary motor cortex BA4p L
+50,GM Primary motor cortex BA4p R
+51,GM Primary somatosensory cortex BA1 L
+52,GM Primary somatosensory cortex BA1 R
+53,GM Primary somatosensory cortex BA2 L
+54,GM Primary somatosensory cortex BA2 R
+55,GM Primary somatosensory cortex BA3a L
+56,GM Primary somatosensory cortex BA3a R
+57,GM Primary somatosensory cortex BA3b L
+58,GM Primary somatosensory cortex BA3b R
+59,GM Secondary somatosensory cortex / Parietal operculum OP1 L
+60,GM Secondary somatosensory cortex / Parietal operculum OP1 R
+61,GM Secondary somatosensory cortex / Parietal operculum OP2 L
+62,GM Secondary somatosensory cortex / Parietal operculum OP2 R
+63,GM Secondary somatosensory cortex / Parietal operculum OP3 L
+64,GM Secondary somatosensory cortex / Parietal operculum OP3 R
+65,GM Secondary somatosensory cortex / Parietal operculum OP4 L
+66,GM Secondary somatosensory cortex / Parietal operculum OP4 R
+67,GM Superior parietal lobule 5Ci L
+68,GM Superior parietal lobule 5Ci R
+69,GM Superior parietal lobule 5L L
+70,GM Superior parietal lobule 5L R
+71,GM Superior parietal lobule 5M L
+72,GM Superior parietal lobule 5M R
+73,GM Superior parietal lobule 7A L
+74,GM Superior parietal lobule 7A R
+75,GM Superior parietal lobule 7M L
+76,GM Superior parietal lobule 7M R
+77,GM Superior parietal lobule 7PC L
+78,GM Superior parietal lobule 7PC R
+79,GM Superior parietal lobule 7P L
+80,GM Superior parietal lobule 7P R
+81,GM Visual cortex V1 BA17 L
+82,GM Visual cortex V1 BA17 R
+83,GM Visual cortex V2 BA18 L
+84,GM Visual cortex V2 BA18 R
+85,GM Visual cortex V3V L
+86,GM Visual cortex V3V R
+87,GM Visual cortex V4 L
+88,GM Visual cortex V4 R
+89,GM Visual cortex V5 L
+90,GM Visual cortex V5 R
+91,GM Premotor cortex BA6 L
+92,GM Premotor cortex BA6 R
+93,WM Acoustic radiation R
+94,WM Acoustic radiation L
+95,WM Callosal body
+96,WM Cingulum R
+97,WM Cingulum L
+98,WM Corticospinal tract R
+99,WM Corticospinal tract L
+100,WM Fornix
+101,WM Inferior occipito-frontal fascicle R
+102,WM Inferior occipito-frontal fascicle L
+103,GM Lateral geniculate body R
+104,GM Lateral geniculate body L
+105,GM Mamillary body
+106,GM Medial geniculate body R
+107,GM Medial geniculate body L
+108,WM Optic radiation R
+109,WM Optic radiation L
+110,WM Superior longitudinal fascicle R
+111,WM Superior longitudinal fascicle L
+112,WM Superior occipito-frontal fascicle R
+113,WM Superior occipito-frontal fascicle L
+114,WM Uncinate fascicle R
+115,WM Uncinate fascicle L
+116,GM Insula Id1 L
+117,GM Insula Id1 R
+118,GM Insula Ig1 L
+119,GM Insula Ig1 R
+120,GM Insula Ig2 L
+121,GM Insula Ig2 R

make_image_from_bin.py

@@ -1,19 +1,36 @@
 #### make_image_from_bin.py
 # Copyright (C) 2010 R. Cameron Craddock ([email protected])
 #
-# This script is a part of the pyClusterROI python toolbox for the spatially constrained clustering of fMRI
-# data. It converts a NPY file generated by binfile_parcellation.py, group_binfile_parcellation.py, or 
-# group_mean_binfile_parcellation.npy into a nifti file where each voxels intensity corresponds to the
-# number of the cluster to which it belongs.
+# This script is a part of the pyClusterROI python toolbox for the spatially
+# constrained clustering of fMRI data. It converts a NPY file generated by
+# binfile_parcellation.py, group_binfile_parcellation.py, or
+# group_mean_binfile_parcellation.npy into a nifti file where each voxels
+# intensity corresponds to the number of the cluster to which it belongs.
 #
 # For more information refer to:
 #
-# Craddock, R. C., James, G. A., Holtzheimer, P. E., Hu, X. P., & Mayberg, H. S. (2011). A whole 
-# brain fMRI atlas generated via spatially constrained spectral clustering. Human brain mapping, 
-# doi: 10.1002/hbm.21333.
+# Craddock, R. C.; James, G. A.; Holtzheimer, P. E.; Hu, X. P. & Mayberg, H. S.
+# A whole brain fMRI atlas generated via spatially constrained spectral
+# clustering Human Brain Mapping, 2012, 33, 1914-1928 doi: 10.1002/hbm.21333.
 #
-# Documentation, updated source code and other information can be found at the NITRC web page:
-# http://www.nitrc.org/projects/cluster_roi/
+# ARTICLE{Craddock2012,
+#   author = {Craddock, R C and James, G A and Holtzheimer, P E and Hu, X P and
+#   Mayberg, H S},
+#   title = {{A whole brain fMRI atlas generated via spatially constrained
+#   spectral clustering}},
+#   journal = {Human Brain Mapping},
+#   year = {2012},
+#   volume = {33},
+#   pages = {1914--1928},
+#   number = {8},
+#   address = {Department of Neuroscience, Baylor College of Medicine, Houston,
+#       TX, United States},
+#   pmid = {21769991},
+# } 
+#
+# Documentation, updated source code and other information can be found at the
+# NITRC web page: http://www.nitrc.org/projects/cluster_roi/ and on github at
+# https://github.com/ccraddock/cluster_roi
 #
 #
 # This program is free software: you can redistribute it and/or modify
@@ -30,50 +47,50 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 ####
 
-# this scripts requires NumPy (numpy.scipy.org), and PyNIfTI 
-# (http://niftilib.sourceforge.net/pynifti/) to be installed in a directory that is
-# accessible through PythonPath 
-from nifti import NiftiImage 
+# this scripts requires NumPy (numpy.scipy.org), and NiBabel
+# (http://niftilib.sourceforge.net/pynifti/) to be installed in a directory
+# that is accessible through PythonPath 
+import nibabel as nb
 from numpy import *
 
 # make_image_from_bin( image, binfile, mask )
 # 
-# Converts a NPY file generated by binfile_parcellation.py, group_binfile_parcellation.py, or 
-# group_mean_binfile_parcellation.npy into a nifti file where each voxels intensity corresponds to the
-# number of the cluster to which it belongs.
+# Converts a NPY file generated by binfile_parcellation.py,
+# group_binfile_parcellation.py, or group_mean_binfile_parcellation.npy into a
+# nifti file where each voxels intensity corresponds to the number of the
+# cluster to which it belongs.
 #     image:   The name of the nifti file to be written.
-#     binfile: The binfile to be converted. The file contains a n_voxel x 1 vector that is
-#              converted to a nifti file.
-#     mask:    Mask describing the space of the nifti file. This should correspond to the 
-#              mask originally used to create the connectivity matrices used for parcellation.
+#     binfile: The binfile to be converted. The file contains a n_voxel x 1
+#              vector that is converted to a nifti file.
+#     mask:    Mask describing the space of the nifti file. This should
+#              correspond to the mask originally used to create the
+#              connectivity matrices used for parcellation.
 #
 def make_image_from_bin( image, binfile, mask ):
 
-	# read in the mask
-	nim=NiftiImage(mask)
-	sz=shape(nim.data)
+    # read in the mask
+    nim=nb.load(mask)
+
+    # read in the binary data    
+    if( binfile.endswith(".npy") ):
+        print "Reading",binfile,"as a npy filetype"
+        a=load(binfile)
+    else:
+        print "Reading",binfile,"as a binary file of doubles"
+        a=fromfile(binfile)
+
+    imdat=nim.get_data()
+    print "shape",shape(a)
+    print "sum",sum(imdat)
 
-        # read in the binary data	
-        # a=fromfile(binfile,'uint32')
-	if( binfile.endswith(".npy") ):
-		print "Reading",binfile,"as a npy filetype"
-		a=load(binfile)
-		#a=((a.tolist()).toarray())[:,0]
-	else:
-		print "Reading",binfile,"as a binary file of doubles"
-        	a=fromfile(binfile)
+    # map the binary data to mask
+    print "shape2",shape(a[0:sum(imdat)])
+    imdat[imdat>0]=short(a[0:sum(imdat)].flatten())
 
-        imdat=nim.data
-	print "shape",shape(a)
-        print "sum",sum(imdat)
-        # map the binary data to mask
-	print "shape2",shape(a[0:sum(imdat)])
-        imdat[imdat>0]=short(a[0:sum(imdat)].flatten())
+    # write out the image as nifti
+    thdr=nim.header
+    thdr['scl_slope']=1
 
-        # write out the image as nifti
-        thdr=nim.header
-        thdr['scl_slope']=1
-
-	nim_out=NiftiImage(imdat)
-	nim_out.updateFromDict(thdr)
-	nim_out.save(image)
+    nim_out = nb.Nifti1Image(imdat, nim.get_affine())
+    nim_out.set_data_dtype('int16')
+    nim_out.to_filename(image)