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top

Striatal Parcellation Estimated by Intrinsic Functional Connectivity

Data from 1000 young healthy adults were registered using nonlinear deformation of the striatum in combination with surface-based alignment of the cerebral cortex. All data were acquired on Siemens 3T scanners using the same functional and structural sequences. A clustering approach was employed to identify and replicate networks of functionally coupled regions across the cerebral cortex (see Yeo et al. 2011). The complete topography of the striatum was then mapped by estimating the principal cerebral target for each voxel in the striatum. The majority of the human striatum maps to association areas. Furthermore, the extent of the cerebellum dedicated to each network is proportional to the network’s extent in the cerebrum with a few exceptions including primary visual cortex. Like somatomotor representations, cerebellar regions linked to association cortex have separate anterior and posterior representations that are oriented as mirror images of one another.

The striatal volumes in which each striatal voxel is assigned to a cerebral network (using either the 7 or 17 network solution in Yeo et al. 2011) are available for download here.

References

Choi EY, Yeo BT, Buckner RL (2012) The organization of the human striatum estimated by intrinsic functional connectivity. J Neurophysiol. In Press.

Buckner RL, Krienen FM, Castellanos A, Diaz JC, Yeo BT (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. The organization of the human cerebral cortex estimated by intrinsic functional connectivity. J Neurophysiol 106(3):1125-65, 2011

Striatal Parcellations in Nonlinear MNI152 Space

7 Network Estimate - Cerebral Cortex

7 Network Estimate - Striatum

Yeo2011_JNeurophysiol_7networks_lateral.png

Choi2012_JNeurophysiol_7Network_striatum_coronal_12.png

Choi2012_JNeurophysiol_7Network_striatum_sagittal_-12.png

Choi2012_JNeurophysiol_7Network_striatum_axial_-2.png

17 Network Estimate - Cerebral Cortex

17 Network Estimate - Striatum

Yeo2011_JNeurophysiol_17networks_lateral.png

Choi2012_JNeurophysiol_17Network_striatum_coronal_12.png

Choi2012_JNeurophysiol_17Network_striatum_sagittal_-12.png

Choi2012_JNeurophysiol_17Network_striatum_axial_-2.png

Downloads

Resting State Striatal Parcellation in FSL MNI152 space. (5.2 Mb download).

Information about Downloads

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. The slices of this volume are shown in Choi et al., 2012.

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).

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:

  • Index

    Network Name

    R

    G

    B

  • 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 nifty values corresponding to the particular network. The second column f the text file specifies the named of the networks. For example, from the text file, voxels whose values = 3 corresponds to the network 7Networks_3.Columns 3 to 5 corresponds 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. The slices of this volume are shown in Choi et al., 2012.

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).

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:

  • Index

    Network Name

    R

    G

    B

  • 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

    200

    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

See README in unzipped folder.

7 Network Tight Mask

7 Network Liberal Mask

17 Network Tight Mask

17 Network Liberal Mask

1) Except for the colortables, all the volumes are nifty 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_LooseMask.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_LooseMask.nii.gz:colormap=lut:lut=Choi2012_7Networks_ColorLUT.txt Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz:colormap=heat:heatscale=0,0.3,0.6

Other downloads

Cerebral Surface Parcellations in FreeSurfer Space

Cerebral Surface Parcellations in FSL MNI152 1mm Volumetric Space

Cerebral Surface Parcellations in Caret Space

Movies of Striatal Seed-based Functional Connectivity

Movies of Cortical Seed-based Functional Connectivity

Code for the von Mises-Fisher Mixture Model Clustering

StriatumParcellation_Choi2012 (last edited 2012-07-27 05:33:24 by ThomasYeo)