Background
==========
Resting state fMRI data from 1000 young healthy adults were registered using nonlinear deformation of the striatum in combination with surface-based alignment of the cerebral cortex. We mapped the complete topography of the striatum by estimating the principal cerebral target for each voxel in the striatum. The parcellations agree with prior models based on monkey anatomy that divide the striatum into broad functional territories of reward, cognition, and motor function. The majority of the human striatum maps to cerebral association areas, with distinct zones of the striatum coupling to distributed regions of large-scale association networks.

Files in Folder (Excluding README)
==================================
1)  FSL_MNI152_FreeSurferConformed_1mm.nii.gz
2)  Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
3)  Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
4)  Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
5)  Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
6)  Choi2012_7Networks_ColorLUT.txt
7)  Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
8)  Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
9)  Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz
10) Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz
11) Choi2012_17Networks_ColorLUT.txt

Descriptions of files
=====================
1) FSL_MNI152_FreeSurferConformed_1mm.nii.gz is the FSL MNI152 1mm template interpolated and intensity normalized into a 256 x 256 x 256 1mm-isotropic volume (obtained by putting the FSL MNI152 1mm template through recon-all using FreeSurfer 4.5.0)

2) Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz is a volume where each striatal voxel was assigned to the cerebral network (out of 7 cerebral networks estimated in Yeo et al., 2011) with the most similar pattern of connectivity.

3) Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz is a volume where each striatal voxel was assigned to the cerebral network (out of 7 cerebral networks estimated in Yeo et al., 2011) with the most similar pattern of connectivity. Here, the striatal mask is tighter than in (2). The slices of this volume are shown in Choi et al., 2012.

4) Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz displays the confidence of the network assignment in Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz.

5) Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz displays the confidence of the network assignment in Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz.

6) Choi2012_7Networks_ColorLUT.txt is a FreeSurfer readable text file specifying how the 7 networks are named, numbered and colored in Choi et al., 2012: 

  0            NONE   0   0   0   0
  1     7Networks_1 120  18 134   0
  2     7Networks_2  70 130 180   0
  3     7Networks_3   0 118  14   0
  4     7Networks_4 196  58 250   0
  5     7Networks_5 220 248 164   0
  6     7Networks_6 230 148  34   0
  7     7Networks_7 205  62  78   0

In particular the networks are numbered from 7Networks_1 to 7Networks_7. The first column of the text file specifies the value of voxels in the nifti values corresponding to the particular network. The second column of the text file specifies the name of the networks. For example, from the text file, voxels whose values = 3 corresponds to the network 7Networks_3. Columns 3 to 5 correspond to the R, G, B values (ranges from 0 to 55) of the networks. Last column is all zeros (FreeSurfer's default).

7) Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz is a volume where each striatal voxel was assigned to the cerebral network (out of 17 cerebral networks estimated in Yeo et al., 2011) with the most similar pattern of connectivity.

8) Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz is a volume where each striatal voxel was assigned to the cerebral network (out of 17 cerebral networks estimated in Yeo et al., 2011) with the most similar pattern of connectivity. Here, the striatal mask is tighter than in (7). The slices of this volume are shown in Choi et al., 2012.

9) Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz displays the confidence of the network assignment in Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz.

10) Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz displays the confidence of the network assignment in Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz.

11) Choi2012_17Networks_ColorLUT.txt is a FreeSurfer readable text file specifying how the 17 networks are named, numbered and colored in Choi et al., 2012:

  0            NONE   0   0   0   0
  1    17Networks_1 120  18 134   0
  2    17Networks_2 255   0   0   0
  3    17Networks_3  70 130 180   0
  4    17Networks_4  42 204 164   0
  5    17Networks_5  74 155  60   0
  6    17Networks_6   0 118  14   0
  7    17Networks_7 196  58 250   0
  8    17Networks_8 255 152 213   0
  9    17Networks_9 220 248 164   0
 10   17Networks_10 122 135  50   0
 11   17Networks_11 119 140 176   0
 12   17Networks_12 230 148  34   0
 13   17Networks_13 135  50  74   0
 14   17Networks_14  12  48 255   0
 15   17Networks_15   0   0 130   0
 16   17Networks_16 255 255   0   0
 17   17Networks_17 205  62  78   0


Example Usage
=============
1) Except for the colortables, all the volumes are nifti volumes which can be read using any software like freeview (FreeSurfer), fslview (FSL), etc.

2) To overlay the 7-network volume on the FSL MNI152 1mm template in freeview (assuming FreeSurfer is already installed) with the appropriate colors, type the following assuming the working directory is in the same directory as the README:

freeview -v FSL_MNI152_FreeSurferConformed_1mm.nii.gz Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz:colormap=lut:lut=Choi2012_7Networks_ColorLUT.txt

3) To overlay the 7-network volume and the confidence of the network assignments on the FSL MNI152 1mm template in freeview (assuming FreeSurfer is already installed) with the appropriate colors, type the following assuming the working directory is in the same directory as the README:

freeview -v FSL_MNI152_FreeSurferConformed_1mm.nii.gz Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz:colormap=lut:lut=Choi2012_7Networks_ColorLUT.txt Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz:colormap=heat:heatscale=0,0.5,1 


Other Downloads
===============
1) Striatum seed-based fcMRI movies can be download here: http://www.youtube.com/choiyeobuckner

2) The cerebral surface parcellations in Caret space can be viewed using Webcaret here: http://sumsdb.wustl.edu:8081/sums/directory.do?id=8286317
   The cerebral surface parcellations in FreeSurfer space can also be downloaded here: http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011
   The cerebral surface parcellations in FSL MNI152 1mm volumetric space can be downloaded here: http://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011
   Cerebral seed-based fcMRI movies can be watched here: http://www.youtube.com/YeoKrienen

3) The cerebellum parcellations in FSL MNI152 1mm volumetric space can be downloaded here: http://surfer.nmr.mgh.harvard.edu/fswiki/CerebellumParcellation_Buckner2011
   Cerebellum seed-based fcMRI movies can be watched here: http://www.youtube.com/BucknerKrienen

References
==========
Choi EY, Yeo BT, Buckner RL (2012) The organization of the human striatum estimated by intrinsic functional connectivity. J Neurophysiol. In Press.
Paper can be downloaded from PubMed here: http://www.ncbi.nlm.nih.gov/pubmed/22832566

Buckner RL, Krienen FM, Castellanos A, Diaz JC, Yeo BTT (2011) The organization of the human cerebellum estimated by intrinsic functional connectivity. J. Neurophysiol. 106(5):2322-45, 2011.

Yeo BT, Krienen FM, Sepulcre J, Sabuncu MR, Lashkari D, Hollinshead M, Roffman JL, Smoller JW, Zollei L., Polimeni JR, Fischl B, Liu H, Buckner RL (2011) The organization of the human cerebral cortex estimated by intrinsic functional connectivity. J. Neurophysiol. 106(3):1125-65, 2011.



