May I ask is there any elegant AFNI approach to combine the left and right hemisphere surface time series and annotation *.niml.dset files?
I am trying to generate a 148x148 functional connectivity matrix using 3dNetCorr for 148 surface ROIs, 74 per each hemisphere defined in std.141.lh/rh.aparc.2009s.annot.niml.dset. The 3D+time residual data from afni_proc.py was converted to surface data using 3dVol2Surf, which had to be done per hemisphere too. Now I have the ROI file and time series data for each hemisphere. I can generate 74x74 matrix for each hemisphere but the inter-hemisphere functional connectivity information is missing.
I am very new to AFNI and I have tried several approaches based on some relevant messages, such as converting to gifti format and manipulating the data using AFNI or FreeSurfer commends, the ones I have tried were ConvertDset, ConvertSurf, gifti_tool, mri_convert, mris_convert, mri_concat, 3dBucket, 3dmerge. Unfortunately, I wasn’t able to concatenate the two hemisphere data and generate the 148x148 matrix.
The only thing I could think now is to write out the time series for each ROI and do the correlation in MATLAB with a fixed ROI label/annotation. Since I need to batch process many datasets, I would highly appreciate if there is an AFNI (or FreeSurfer) approach so that the process can be fully automated and take advantage of other AFNI tools for further analysis.
Thank you in advance for any help.