I am using the Schaefer 400 parcels (17 networks) atlas as my ROIs for tractography using 3DTrackID. Here is my current workflow:
mri_surf2surf --> resample Schaefer parcellation from fsaverage subject onto subject of interest
FSread_annot --> convert annot file to Suma-usable niml.dset format
SurfToSurf --> register niml.dset from original surface onto standard mesh of linear density 20, 60, and 141
fat_proc_map_to_dti --> align standard mesh niml.dset data to DTI space
3dSurf2Vol -->map surface data to volume using "mode" map_func along smoothwm
3dROIMaker --> grow volumetric parcels based on wm_skeleton of dt_FA according to 0.2 threshold
The main problem with this workflow is that the Schaefer volumetric ROIs that I am creating are extremely irregular and do not look great. I also haven't loaded in the atlases, so I cannot use the whereami function. I noticed that you have released a new Schaefer atlas this year in MNI152_2009 space. I'm not sure how to incorporate these files into my set-up. Can I use the nii.gz files that you provided and transform those into my DTI space and then run 3dtrackid with those parcels? Or should I use the std141*niml.dset files that you provided and use SurfToSurf to register those with my subject and then continue with my previous workflow? I would like to eventually get to a point where I have niml.dset files to view these parcels on the surface but also volumetric files to run 3dtrackID with.
I am very new to AFNI, but I have watched all of the MIT bootcamp videos on DTI/FATCAT, SUMA, and ROIs/Atlases. Yet, I still feel confused on how to transform all of these files, and I am working with a pipeline that was made before I joined the project. Any help will be appreciated! Thanks.
