CPAC outputs for RBC

Software Support
,
1

Hi,

I got a few questions about the CPAC output files for the PNC dataset available on RBC: PNC_CPAC/cpac_RBCv0 at main · ReproBrainChart/PNC_CPAC · GitHub
Here is the CPAC config file specific to RBC: C-PAC/CPAC/resources/configs/pipeline_config_rbc-options.yml at 0182f98c61cb7fbb495c8300e6a6a7991c859240 · FCP-INDI/C-PAC · GitHub

I’m looking under subdirectory subject/ses-PNC1/func/:

I’d like to understand differences in field of view for derivative maps across subjects. In other words, how does availability of the measure at each point in the MNI space vary across subjects? Taking ALFF maps as an example, I narrowed down to files whose names start with “sub-xxx_ses-PNC1_task-rest_acq-singleband_space-MNI152NLin6ASym_”. Here are my questions:

  1. Are all the derivatives for the same subject (alff, dcb, falff, lfcdv, lfcdw, reho) generated using the same mask (desc-bold_mask.nii.gz)? i.e. the availability of voxel levels should be the same for the derivative maps of a single subject?

  2. If I want to create an average ALFF map for all subjects, is it safe to first create a group-level mask (e.g. include voxels that are available in >0.8 of subjects), directly take an average over “…desc-sm6_alff.json”, apply the group mask, and then z-standardize the averaged map?

I’d very much appreciate any suggestions / insights!

2

Hi @yhao,

Great questions. Here are some thoughts-

For the first question:

  • Yes, C-PAC will generate a BOLD mask based on your configuration and will use that same mask for all downstream BOLD-derived data.
  • The mask that is created and used will depend on your configuration - if you are calculating the derivatives in native BOLD space, it will use the original BOLD mask that is created. If you are calculating the derivatives in template space, it will use a version of the BOLD mask that has been transformed to template space at the resolution specified in your config for derivative outputs.
  • If you are forking the BOLD mask options and producing multiple, you will get a set of derivative outputs for each mask.
  • Either way, it will always be the same mask across derivatives.

For the second question:

  • Based on the filename sample you mentioned earlier, I’m assuming you intend to do this with the template-space version of the ALFF maps, which would be advisable. If this is the case, I believe this approach is sound. Please feel free to reach out if you have any other questions or ideas, we’re always happy to hear about how our community uses our tools for research!

Best,
Steve G.