Atlas Lookup via MNI-coordinate

scripts/atlas_reader.py

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+import sys
+import numpy as np
+import nibabel as nb
+
+
+def getVoxCoord(affine, coord):
+    """computes voxel ID from MNI coordinate"""
+    inverse = np.linalg.inv(affine)
+    voxCoord = np.dot(inverse, np.hstack((coord, 1)))[:3]
+    return voxCoord.round().astype('int').tolist()
+
+
+def getLabel(atlastype, labelID):
+    """reads out the name of a specific label"""
+    if 'freesurfer' in atlastype:
+        atlastype = 'freesurfer'
+    labels = np.recfromcsv('../scripts/atlases/labels_%s.csv' % atlastype)
+    labelIdx = labels.index == labelID
+    if labelIdx.sum() == 0:
+        label = 'No_label'
+    else:
+        label = labels[labelIdx][0][1]
+    return label
+
+
+def readAtlas(atlastype, coordinate, probThresh=5):
+    """
+    Reads specific atlas and returns segment/probability information.
+    It is possible to threshold a given probability atlas [in percentage].
+    """
+
+    if atlastype in ['aal',
+                     'freesurfer_desikan-killiany',
+                     'freesurfer_destrieux']:
+        atlas = nb.load('../scripts/atlases/atlas_%s.mgz' % atlastype)
+        probAtlas = False
+    else:
+        atlas = nb.load('../scripts/atlases/atlas_%s.nii.gz' % atlastype)
+        probAtlas = True
+
+    # Get atlas data and affine matrix
+    data = atlas.get_data()
+    affine = atlas.get_affine()
+
+    # Get voxel index
+    voxID = getVoxCoord(affine, coordinate)
+
+    # Get Label information
+    if probAtlas:
+        probs = data[voxID[0], voxID[1], voxID[2]]
+        probs[probs < probThresh] = 0
+        idx = np.where(probs)[0]
+
+        # sort list by probability
+        idx = idx[np.argsort(probs[idx])][::-1]
+
+        # get probability and label names
+        probLabel = []
+        for i in idx:
+            label = getLabel(atlastype, i)
+            probLabel.append([probs[i], label])
+
+        # If no labels found
+        if probLabel == []:
+            probLabel = [[0, 'No_label']]
+
+        return probLabel
+
+    else:
+        labelID = int(data[voxID[0], voxID[1], voxID[2]])
+        label = getLabel(atlastype, labelID)
+        return label
+
+
+def writeOutputToScreen(atlasinfo, coord):
+    """Writes output to the sceen"""
+    print "Segmentation information at {0}:".format(coord)
+
+    for ainfo in atlasinfo:
+        if ainfo[0] in ['aal',
+                        'freesurfer_desikan-killiany',
+                        'freesurfer_destrieux']:
+            print "{0:<36}{1}".format(ainfo[0], ainfo[1])
+        else:
+            for s in ainfo[1]:
+                print "{0:<30}{1:>4}% {2}".format(ainfo[0], s[0], s[1])
+    print "\n"
+
+
+def getAtlasinfo(coord, atlastype='all', probThresh=5, writeToScreen=True):
+
+    atlasinfo = []
+    if atlastype != 'all':
+        segment = readAtlas(atlastype, coord, probThresh)
+        atlasinfo.append([atlastype, segment])
+    else:
+        for atypes in ['aal',
+                       'freesurfer_desikan-killiany',
+                       'freesurfer_destrieux',
+                       'HarvardOxford',
+                       'Juelich']:
+            segment = readAtlas(atypes, coord, probThresh)
+            atlasinfo.append([atypes, segment])
+
+    # Write output to screen
+    if writeToScreen:
+        writeOutputToScreen(atlasinfo, coord)
+
+    return atlasinfo
+
+
+if __name__ == "__main__":
+
+    atlastype = str(sys.argv[1])
+    coord = [float(x) for x in str(sys.argv[2]).split(',')]
+    probThresh = int(sys.argv[3])
+    writeToScreen = bool(sys.argv[4])
+
+    getAtlasinfo(coord, atlastype, probThresh, writeToScreen)

scripts/atlases/description_HarvardOxford.rst

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+Harvard-Oxford atlas
+--------------------
+
+The Harvard-Oxford cortical and subcortical structural atlases are a copy of
+FSL's (Version 5.0) under `$FSL_DIR/data/atlases/HarvardOxford/`:
+ - HarvardOxford-cortl-prob-1mm.nii.gz' 
+ - HarvardOxford-sub-prob-1mm.nii.gz' 
+For further information see http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases.
+
+The following 4 areas were deleted from the subcortical structural atlas, as
+they are already coverd in the cortical structural atlas:
+ - 'Left Cerebral White Matter'
+ - 'Left Cerebral Cortex '
+ - 'Right Cerebral White Matter'
+ - 'Right Cerebral Cortex '
+
+Afterwards, the cortical and subcortical structural atlases were merged with
+the following python code:
+
+    import nibabel as nb
+    cort = nb.load('HarvardOxford-cort-prob-1mm.nii.gz')
+    sub = nb.load('HarvardOxford-sub-prob-1mm.nii.gz')
+    newsubdata = sub.get_data()[:, :, :, range(2, 11) + range(13, 21)]
+    data = np.concatenate((cort.get_data(), newsubdata), axis=3)
+    affine = cort.get_affine()
+    nb.Nifti1Image(data.astype('uint8'), affine).to_filename('bladi.nii.gz')
+
+
+References
+----------
+
+Makris N, Goldstein JM, Kennedy D, Hodge SM, Caviness VS, Faraone SV, Tsuang MT, Seidman LJ. Decreased volume of left and total anterior insular lobule in schizophrenia. Schizophr Res. 2006 Apr;83(2-3):155-71
+
+Frazier JA, Chiu S, Breeze JL, Makris N, Lange N, Kennedy DN, Herbert MR, Bent EK, Koneru VK, Dieterich ME, Hodge SM, Rauch SL, Grant PE, Cohen BM, Seidman LJ, Caviness VS, Biederman J. Structural brain magnetic resonance imaging of limbic and thalamic volumes in pediatric bipolar disorder. Am J Psychiatry. 2005 Jul;162(7):1256-65
+
+Desikan RS, Ségonne F, Fischl B, Quinn BT, Dickerson BC, Blacker D, Buckner RL, Dale AM, Maguire RP, Hyman BT, Albert MS, Killiany RJ. An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. Neuroimage. 2006 Jul 1;31(3):968-80.
+
+Goldstein JM, Seidman LJ, Makris N, Ahern T, O'Brien LM, Caviness VS Jr, Kennedy DN, Faraone SV, Tsuang MT. Hypothalamic abnormalities in schizophrenia: sex effects and genetic vulnerability. Biol Psychiatry. 2007 Apr 15;61(8):935-45

scripts/atlases/description_Juelich.txt

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+Juelich atlas
+--------------
+
+The Juelich atlas is a direct copy of FSL's (Version 5.0) Juelich atlas under
+`$FSL_DIR/data/atlases/Juelich/Juelich-prob-1mm.nii.gz`.
+For further information see http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlases.
+
+
+References
+----------
+
+Eickhoff, S. B., Stephan, K. E., Mohlberg, H., Grefkes, C., Fink, G. R., Amunts, K., & Zilles, K. (2005). A new SPM toolbox for combining probabilistic cytoarchitectonic maps and functional imaging data. Neuroimage, 25(4), 1325-1335.
+
+Eickhoff, S. B., Heim, S., Zilles, K., & Amunts, K. (2006). Testing anatomically specified hypotheses in functional imaging using cytoarchitectonic maps. Neuroimage, 32(2), 570-582.
+
+Eickhoff, S. B., Paus, T., Caspers, S., Grosbras, M. H., Evans, A. C., Zilles, K., & Amunts, K. (2007). Assignment of functional activations to probabilistic cytoarchitectonic areas revisited. Neuroimage, 36(3), 511-521.

scripts/atlases/description_aal.txt

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+AAL atlas
+---------
+
+The Anatomical Automatic Labeling (AAL) atlas is a copy of SPM12's AAL atlas
+(from 25/08/2015) that can be found here: http://www.gin.cnrs.fr/spip-php-article217
+
+The NIfTI file was converted into MGZ-file format with the following command:
+
+    mri_convert aal_SPM12/AAL.nii aal.mgz
+
+
+References
+----------
+
+Tzourio-Mazoyer, N., Landeau, B., Papathanassiou, D., Crivello, F., Etard, O., Delcroix, N., ... & Joliot, M. (2002). Automated anatomical labeling of activations in SPM using a macroscopic anatomical parcellation of the MNI MRI single-subject brain. Neuroimage, 15(1), 273-289.

scripts/atlases/description_freesurfer.txt

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+FreeSurfer atlas
+----------------
+
+The following two atlases are a copy from FreeSurfer's (v5.3.) subject folder
+`cvs_avg35_inMNI152` under `$FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri`:
+ - Desikan-Killiany atlas was renamed from aparc+aseg.mgz to
+   atlas_freesurfer_desikan-killiany.mgz
+ - Destrieux atlas was renamed from aparc.a2009s+aseg.mgz to
+   atlas_freesurfer_destrieux.mgz
+
+
+References
+----------
+
+Fischl, B., van der Kouwe, A., Destrieux, C., Halgren, E., Ségonne, F., Salat, D. H., ... & Caviness, V. (2004). Automatically parcellating the human cerebral cortex. Cerebral cortex, 14(1), 11-22.
+
+Destrieux, C., Fischl, B., Dale, A. M., & Halgren, E. (2009). A sulcal depth-based anatomical parcellation of the cerebral cortex. NeuroImage, 47, S151.
+
+Desikan, R. S., Ségonne, F., Fischl, B., Quinn, B. T., Dickerson, B. C., Blacker, D., ... & Albert, M. S. (2006). An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. Neuroimage, 31(3), 968-980.

scripts/atlases/labels_HarvardOxford.csv

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+index,name
+0,Frontal_Pole
+1,Insular_Cortex
+2,Superior_Frontal_Gyrus
+3,Middle_Frontal_Gyrus
+4,Inferior_Frontal_Gyrus_pars_triangularis
+5,Inferior_Frontal_Gyrus_pars_opercularis
+6,Precentral_Gyrus
+7,Temporal_Pole
+8,Superior_Temporal_Gyrus_anterior_division
+9,Superior_Temporal_Gyrus_posterior_division
+10,Middle_Temporal_Gyrus_anterior_division
+11,Middle_Temporal_Gyrus_posterior_division
+12,Middle_Temporal_Gyrus_temporooccipital_part
+13,Inferior_Temporal_Gyrus_anterior_division
+14,Inferior_Temporal_Gyrus_posterior_division
+15,Inferior_Temporal_Gyrus_temporooccipital_part
+16,Postcentral_Gyrus
+17,Superior_Parietal_Lobule
+18,Supramarginal_Gyrus_anterior_division
+19,Supramarginal_Gyrus_posterior_division
+20,Angular_Gyrus
+21,Lateral_Occipital_Cortex_superior_division
+22,Lateral_Occipital_Cortex_inferior_division
+23,Intracalcarine_Cortex
+24,Frontal_Medial_Cortex
+25,Juxtapositional_Lobule_Cortex_(formerly_Supplementary_Motor_Cortex)
+26,Subcallosal_Cortex
+27,Paracingulate_Gyrus
+28,Cingulate_Gyrus_anterior_division
+29,Cingulate_Gyrus_posterior_division
+30,Precuneous_Cortex
+31,Cuneal_Cortex
+32,Frontal_Orbital_Cortex
+33,Parahippocampal_Gyrus_anterior_division
+34,Parahippocampal_Gyrus_posterior_division
+35,Lingual_Gyrus
+36,Temporal_Fusiform_Cortex_anterior_division
+37,Temporal_Fusiform_Cortex_posterior_division
+38,Temporal_Occipital_Fusiform_Cortex
+39,Occipital_Fusiform_Gyrus
+40,Frontal_Operculum_Cortex
+41,Central_Opercular_Cortex
+42,Parietal_Operculum_Cortex
+43,Planum_Polare
+44,Heschl's_Gyrus_(includes_H1_and_H2)
+45,Planum_Temporale
+46,Supracalcarine_Cortex
+47,Occipital_Pole
+48,Left_Lateral_Ventrical
+49,Left_Thalamus
+50,Left_Caudate
+51,Left_Putamen
+52,Left_Pallidum
+53,Brain-Stem
+54,Left_Hippocampus
+55,Left_Amygdala
+56,Left_Accumbens
+57,Right_Lateral_Ventricle
+58,Right_Thalamus
+59,Right_Caudate
+60,Right_Putamen
+61,Right_Pallidum
+62,Right_Hippocampus
+63,Right_Amygdala
+64,Right_Accumbens