Names of ROIs

Submitted by Timhahn on Wed, 10/31/2012 - 23:32

 Dear all -
I extracted the connectivity matrix between all ROIs from the atlases provided with DPARSFA (AAL, Craddock, Dosenbach, ...). How do I find out the name of each ROI for each atlas? For the Harvard Oxford Atlas a file with anatomical labels is provided, but I'm not sure on how to use that.
In short, my question is: How do I can the names for the ROIs of the atlases provided with DPARSFA?
Thank you very much for your help.
Cheers,
Tim

Submitted by YAN Chao-Gan on Fri, 11/02/2012 - 10:00

1. AAL Atlas
The AAL atlas is the same as provided in MRIcroN. You can find the details of each region from http://www.restfmri.net/forum/DPARSF_V1_0#comment-373
2. Harvard Oxford Atlas
The atlas is based on the Harvard Oxford atlas files (thresholded at probability 25%) provided in FSL:
HarvardOxford-cort-maxprob-thr25-2mm.nii.gz (cortical)
HarvardOxford-sub-maxprob-thr25-2mm.nii.gz (subcortical)
 
Given the order in the original files were not easy to use in extracting ROI time series (e.g., the left right ROI share the same index), the ROIs were re-indexed as detailed in the {DPARSF}\Templates\HarvardOxford_Atlas_NewIndex_YCG.xlsx
3. Dosenbach 160 ROIs
 
The ROI center is extracted from Table S6 in Dosenbach et al., 2010. Prediction of individual brain maturity using fMRI. Science 329, 1358-1361. The ROIs were summarized from meta-analysis.

ROI Cennter
 

4. Andrews-Hanna’s default mode network ROIs
 
The ROI center is extracted from Table S1 in Andrews-Hanna et al., 2010. Functional-anatomic fractionation of the brain's default network. Neuron 65, 550-562. 
 
5. Craddock’s clustering ROIs 
 
The ROIs were using the ROI files provided in http://www.nitrc.org/projects/cluster_roi/ as described in Craddock et al., 2012. A whole brain fMRI atlas generated via spatially constrained spectral clustering. Hum Brain Mapp 33, 1914-1928. The ROI names were not provided yet from that website.
Center of Mass

Best,

Chao-Gan