Hi Alfonso,
That is tremendously helpful, thank you!!
I had two follow-up questions:
1) In addition to the 32 networks that you have set as default, I would also be interested in performing analyses using the 7 Yeo networks. What would be the proper way to load them into CONN? Based on a prior thread, I gathered that I should break the Freesurfer provided liberal Yeo atlas into its 7 components and merge them into a 4d volume, as in:
rex split Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii
spm_file_merge(spm_vol(char(conn_dir('Yeo*.rex.roi.img','-ls'))),'Yeo2011_template.nii');
, then add the Yeo2011_template.nii file as a new "atlas file" under the ROIs tab, and run the denoising and 1st level analyses (without any need to re-run preprocessing).
<span style="white-space: pre;"><span style="white-space: pre;"> </span>a</span>) Is this approach correct?
<span style="white-space: pre;"> </span>b) Do I need to add an associated text file in the same directory in addition to the Yeo2011_template.nii file? If yes, should that text file be the Yeo2011_7Networks_ColorLUT.txt file located under $FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/ or a different txt file that contains the centroids of each ROI such as the networks.txt file under conn/rois?
2) Assuming that I have connectivity results with the Yeo atlas mentioned above, I would be interested in knowing which voxel IDs (identified from question 4 in the previous message) belong to each of the 7 ROIs. I could think of a way to check that using a for loop that goes through each voxel ID and checks whether its xyz coordinates belong to any of the 7 ROIs, but would you happen to know of a less computationally tedious way to do that?
Thanks again,
Panos
That is tremendously helpful, thank you!!
I had two follow-up questions:
1) In addition to the 32 networks that you have set as default, I would also be interested in performing analyses using the 7 Yeo networks. What would be the proper way to load them into CONN? Based on a prior thread, I gathered that I should break the Freesurfer provided liberal Yeo atlas into its 7 components and merge them into a 4d volume, as in:
rex split Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii
spm_file_merge(spm_vol(char(conn_dir('Yeo*.rex.roi.img','-ls'))),'Yeo2011_template.nii');
, then add the Yeo2011_template.nii file as a new "atlas file" under the ROIs tab, and run the denoising and 1st level analyses (without any need to re-run preprocessing).
<span style="white-space: pre;"><span style="white-space: pre;"> </span>a</span>) Is this approach correct?
<span style="white-space: pre;"> </span>b) Do I need to add an associated text file in the same directory in addition to the Yeo2011_template.nii file? If yes, should that text file be the Yeo2011_7Networks_ColorLUT.txt file located under $FREESURFER_HOME/average/Yeo_JNeurophysiol11_MNI152/ or a different txt file that contains the centroids of each ROI such as the networks.txt file under conn/rois?
2) Assuming that I have connectivity results with the Yeo atlas mentioned above, I would be interested in knowing which voxel IDs (identified from question 4 in the previous message) belong to each of the 7 ROIs. I could think of a way to check that using a for loop that goes through each voxel ID and checks whether its xyz coordinates belong to any of the 7 ROIs, but would you happen to know of a less computationally tedious way to do that?
Thanks again,
Panos