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=== Downloads === ==== Downloads ====
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=== Information about Downloads ===
==== Information about Downloads ====
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==== Example Usage ====
1. Once unzipped, make sure freesurfer has been set up and configured as usual (http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration).

2. In terminal (ASSUMING shell is csh or tcsh),
   a) "cd" to unzipped folder containing this README file, fsaverage, fsaverage6, fsaverage5
   b) setenv SUBJECTS_DIR `pwd`
   c) tksurfer fsaverage5 lh inflated -annotation fsaverage5/label/lh.Yeo2011_7Networks_N1000.annot

3. In terminal (ASSUMING shell is bash),
   a) "cd" to unzipped folder containing this README file, fsaverage, fsaverage6, fsaverage5
   b) export SUBJECTS_DIR=``pwd``
   c) tksurfer fsaverage5 lh inflated -annotation fsaverage5/label/lh.Yeo2011_7Networks_N1000.annot
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=== Downloads ===
[[ftp://surfer.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_FreeSurfer.zip|Resting State Cortical Parcellation in fsaverage, fsaverage6 and fsaverage5 Space]]. These subjects are also currently in the developmental version of FreeSurfer which can be assessed from the Martinos center network (/autofs/cluster/freesurfer/centos4.0_x86_64/dev/subjects/). These subjects will be officially included in some future FreeSurfer release. Note however, the zip file linked here corresponds exactly to that from the reference, while functional parcellations in the developmental and official release versions of FreeSurfer are subjected to modifications/improvements.
==== Downloads ====
[[ftp://surfer.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_MNI152.zip|Resting State Cortical Parcellation in nonlinear MNI152 space]]. We are working to put these subjects in FreeSurfer. Note however, the zip file linked here corresponds exactly to that from the reference, while functional parcellations in the developmental and official release versions of FreeSurfer are subjected to modifications/improvements.
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[[http://www.youtube.com/user/YeoKrienen|Movies of Seed-based Functional Connectivity]] ==== 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)
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=== Information about Downloads ===
There are three folders in "`Yeo_JNeurophysiol11_FreeSurfer.zip`", corresponding to the "fsaverage", "fsaverage5" and "fsaverage6" surface space. "fsaverage" contains the high resolution version of the parcellation, while "fsaverage6" and "fsaverage5" contain lower resolution versions of the parcellation. The parcellations were computed in "fsaverage5" space and upsampled to "fsaverage6" and "fsaverage".
2. `Yeo2011_7Networks_MNI152_FreeSurferConformed1mm.nii.gz` is a volume consisting of 7 cortical networks projected into MNI152 space. The cortical ribbon is defined by putting the FSL MNI152 1mm template through recon-all using FreeSurfer 4.5.0. The slices of this volume is shown in Yeo et al., 2011.
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The structure of each folder follows that of a preprocessed freesurfer subject. In particular, "fsaverage/label/", "fsaverage5/label/", "fsaverage6/label/" contain all the parcellation and confidence files. For example, "fsaverage/label/rh.Yeo2011_7Networks_N1000.annot" is the 7-network parcellation for 1000 subjects on the right hemisphere and "fsaverage/label/lh.Yeo2011_17NetworksConfidence_N1000.mgz" is the confidence map for the 17-network parcellation for 1000 subjects on the left hemisphere. 3. `Yeo2011_7Networks_MNI152_FreeSurferConformed1mm.nii.gz` is a volume consisting of 7 cortical networks projected into MNI152 space. The cortical ribbon is defined in a more liberal fashion than in (2). More specifically, the cortical mask is obtained by nonlinear warping 1000 subjects (from Yeo et al. 2011, Buckner et al. 2011) into MNI152 space via the FreeSurfer recon-all pipeline. An initial mask is first obtained where a vox l is decided to be a cortical voxel if the cortex of more than 150 subjects (out of 1000 subjects) were mapped to the voxel or if the voxel is labeled as part of the cortical ribbon from (2). This cortical mask is th n smoothed, and small holes and islands in the masks are removed by simple morphological operations.

4. Yeo2011_7Networks_ColorLUT.txt is a FreeSurfer readable text file specifying how the 7 networks are named, numbered and colored in Yeo et al. 2011:

  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).

5. `Yeo2011_17Networks_MNI152_FreeSurferConformed1mm.nii.gz` is a volume consisting of 17 cortical networks projected into MNI152 space. The cortical ribbon is defined in the same fashion as (2), i.e., by putting the F L MNI152 1mm template through recon-all using FreeSurfer 4.5.0.

6. `Yeo2011_17Networks_MNI152_FreeSurferConformed1mm.nii.gz` is a volume consisting of 17 cortical networks projected into MNI152 space. The cortical ribbon is defined in a more liberal fashion than in (2) and in the s me way as (3).

7. Yeo2011_17Networks_ColorLUT.txt is a FreeSurfer readable text file specifying how the 17 networks are named, numbered and colored in Yeo et al. 2011:

  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 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 this README:

freeview -v FSL_MNI152_FreeSurferConformed_1mm.nii.gz Yeo2011_7Networks_MNI152_FreeSurferConformed1mm.nii.gz:colormap=lut:lut=Yeo2011_7Networks_ColorLUT.txt
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top

Resting State Cortical Parcellation

Resting state fMRI data from 1000 subjects were registered using surface-based alignment. A clustering approach was employed to identify and replicate networks of functionally coupled regions across the cerebral cortex. The results revealed local networks confined to sensory and motor cortices as well as distributed networks of association regions that form interdigitated circuits. Within the sensory and motor cortices, functional connectivity followed topographic representations across adjacent areas. In association cortex, the connectivity patterns often showed abrupt transitions between network boundaries, forming largely parallel circuits. The parcellations of the cerebral cortex into 7 and 17 networks in FreeSurfer surface space and nonlinear MNI152 are available for download.

References

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. In Press.

Parcellations in FreeSurfer Surface Space

7 Network Estimate

7 Network Confidence

17 Network Estimate

17 Network Confidence

Yeo2011_JNeurophysiol_7networks_lateral.png

Yeo2011_JNeurophysiol_7networks_lateral_confidence.png

Yeo2011_JNeurophysiol_17networks_lateral.png

Yeo2011_JNeurophysiol_17networks_lateral_confidence.png

Yeo2011_JNeurophysiol_7networks_medial.png

Yeo2011_JNeurophysiol_7networks_medial_confidence.png

Yeo2011_JNeurophysiol_17networks_medial.png

Yeo2011_JNeurophysiol_17networks_medial_confidence.png

Downloads

Resting State Cortical Parcellation in fsaverage, fsaverage6 and fsaverage5 Space. These subjects are also currently in the developmental version of FreeSurfer which can be assessed from the Martinos center network (/autofs/cluster/freesurfer/centos4.0_x86_64/dev/subjects/). These subjects will be officially included in some future FreeSurfer release. Note however, the zip file linked here corresponds exactly to that from the reference, while functional parcellations in the developmental and official release versions of FreeSurfer are subjected to modifications/improvements.

Information about Downloads

There are three folders in "Yeo_JNeurophysiol11_FreeSurfer.zip", corresponding to the "fsaverage", "fsaverage5" and "fsaverage6" surface space. "fsaverage" contains the high resolution version of the parcellation, while "fsaverage6" and "fsaverage5" contain lower resolution versions of the parcellation. The parcellations were computed in "fsaverage5" space and upsampled to "fsaverage6" and "fsaverage".

The structure of each folder follows that of a preprocessed freesurfer subject. In particular, "fsaverage/label/", "fsaverage5/label/", "fsaverage6/label/" contain all the parcellation and confidence files. For example, "fsaverage/label/rh.Yeo2011_7Networks_N1000.annot" is the 7-network parcellation for 1000 subjects on the right hemisphere and "fsaverage/label/lh.Yeo2011_17NetworksConfidence_N1000.mgz" is the confidence map for the 17-network parcellation for 1000 subjects on the left hemisphere.

Example Usage

1. Once unzipped, make sure freesurfer has been set up and configured as usual (http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration).

2. In terminal (ASSUMING shell is csh or tcsh),

  • a) "cd" to unzipped folder containing this README file, fsaverage, fsaverage6, fsaverage5

    b) setenv SUBJECTS_DIR pwd c) tksurfer fsaverage5 lh inflated -annotation fsaverage5/label/lh.Yeo2011_7Networks_N1000.annot

3. In terminal (ASSUMING shell is bash),

  • a) "cd" to unzipped folder containing this README file, fsaverage, fsaverage6, fsaverage5

    b) export SUBJECTS_DIR=pwd c) tksurfer fsaverage5 lh inflated -annotation fsaverage5/label/lh.Yeo2011_7Networks_N1000.annot

Parcellations in MNI152 Surface Space

7 Network Tight Mask

7 Network Liberal Mask

17 Network Tight Mask

17 Network Liberal Mask

Yeo2011_JNeurophysiol_7networks_TightMask_axial9.png

Yeo2011_JNeurophysiol_7networks_LiberalMask_axial9.png

Yeo2011_JNeurophysiol_17networks_TightMask_axial9.png

Yeo2011_JNeurophysiol_17networks_LiberalMask_axial9.png

Downloads

Resting State Cortical Parcellation in nonlinear MNI152 space. We are working to put these subjects in FreeSurfer. Note however, the zip file linked here corresponds exactly to that from the reference, while functional parcellations in the developmental and official release versions of FreeSurfer are subjected to modifications/improvements.

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. Yeo2011_7Networks_MNI152_FreeSurferConformed1mm.nii.gz is a volume consisting of 7 cortical networks projected into MNI152 space. The cortical ribbon is defined by putting the FSL MNI152 1mm template through recon-all using FreeSurfer 4.5.0. The slices of this volume is shown in Yeo et al., 2011.

3. Yeo2011_7Networks_MNI152_FreeSurferConformed1mm.nii.gz is a volume consisting of 7 cortical networks projected into MNI152 space. The cortical ribbon is defined in a more liberal fashion than in (2). More specifically, the cortical mask is obtained by nonlinear warping 1000 subjects (from Yeo et al. 2011, Buckner et al. 2011) into MNI152 space via the FreeSurfer recon-all pipeline. An initial mask is first obtained where a vox l is decided to be a cortical voxel if the cortex of more than 150 subjects (out of 1000 subjects) were mapped to the voxel or if the voxel is labeled as part of the cortical ribbon from (2). This cortical mask is th n smoothed, and small holes and islands in the masks are removed by simple morphological operations.

4. Yeo2011_7Networks_ColorLUT.txt is a FreeSurfer readable text file specifying how the 7 networks are named, numbered and colored in Yeo et al. 2011:

  • 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).

5. Yeo2011_17Networks_MNI152_FreeSurferConformed1mm.nii.gz is a volume consisting of 17 cortical networks projected into MNI152 space. The cortical ribbon is defined in the same fashion as (2), i.e., by putting the F L MNI152 1mm template through recon-all using FreeSurfer 4.5.0.

6. Yeo2011_17Networks_MNI152_FreeSurferConformed1mm.nii.gz is a volume consisting of 17 cortical networks projected into MNI152 space. The cortical ribbon is defined in a more liberal fashion than in (2) and in the s me way as (3).

7. Yeo2011_17Networks_ColorLUT.txt is a FreeSurfer readable text file specifying how the 17 networks are named, numbered and colored in Yeo et al. 2011:

  • 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 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 this README:

freeview -v FSL_MNI152_FreeSurferConformed_1mm.nii.gz Yeo2011_7Networks_MNI152_FreeSurferConformed1mm.nii.gz:colormap=lut:lut=Yeo2011_7Networks_ColorLUT.txt

Other downloads

Surface Parcellations in Caret Space

Movies of Seed-based Functional Connectivity

CorticalParcellation_Yeo2011 (last edited 2013-10-14 20:40:25 by ThomasYeo)