Hi everyone. I’m a new user of C-PAC, and intend to use the data of ABIDE preprocessed by C-PAC. I need to calculate the functional connectivity of DMN regions and the gray matter volume of the same regions. I found the already extracted time series of different ROIs of different atlases that I can use, but the already anatomical images have been preprocessed by Freesurfer or ANTs, which utilizes different atlases (DKT) that are not used in the extracted time series part. Could you please let me know if it is possible to do anatomical preprocessing using C-PAC and choose the desired atlases, like AAL or Craddok400, instead of the DKT default atlas? If yes, how can I do this?
Also, I’d be thankful if you have better suggestions for addressing my goal.
Thanks in advance
Hi Maryam,
Sorry about the slow response ― C-PAC is transitioning into maintenance mode and no longer has a dedicated support team.
As far as I know, C-PAC uses atlases for timeseries extraction and seed-based correlation analysis but not for anything anatomical-only.
Also, the preprocessed ABIDE data was generated years ago (version 0.3.9.1 for ABIDE I and a version around 1.0.2 for ABIDE II (I’m not readily finding the documentation for which version was used there)). C-PAC and most of its dependencies have been through many updates in the intervening years, so be mindful of mixing preprocessed data with additional preprocessing.
Can you elaborate what you’re trying to do here?
Hi Jon Clucas,
Thank you so much for replying and for your guidance.
Actually, I want to calculate the gray matter volume and cortical thickness of the ROIs defined by some atlases, like Craddock400, rather than the DKT atlas used by Freesurfer for the parcellation and processing of the anatomical images, because the preprocessed ABIDE data has already provided the mean time series of the ROIs of the Craddock400 atlas using C-PAC. Is it possible by C-PAC (or other software or codes) and how?
As far as I know C-PAC hasn’t ever calculated anatomical ROI measures. I’ll update the issue you opened to a feature request to make this possible with C-PAC, but with the project going into maintenance mode, I expect the feature won’t be added any time soon.
If I’m reading ABIDE Preprocessed correctly, it looks like the cortical anatomical ROI measures were calculated with ANTs and CIVET (both of which are outside my areas of expertise but which you can probably find others on Neurostars with advanced knowledge of both).
The atlases that were used for the ABIDE preprocessed data are available in 
/preprocessed-connectomes-project/abide or from s3://fcp-indi/data/Projects/ABIDE/Resources. The template used was MNI152_T1_2mm_brain.nii.gz from FSL 5. I think from these and the raw or preprocessed anatomical images you should be able to use ANTs and CIVET to calculate those anatomical ROI measures.
Thanks a lot, Jon Clucas. Your advice was so valuable and useful.