Schaefer parcellation gap between parcels with HCP data

[snapfinger]

Hi there, I successfully ran Schaefer parcellation code on HCP resting-state fMRI data of 500 subjects. However, there are gaps between the parcels (see below) consisting of vertices with seemingly random parcel assignment. I wonder why it is like this and if there's a way to adjust it to the type of no-gap parcels from the example (the bottom image)?

I used the following settings in CBIG_gwMRF_build_data_and_perform_clustering.m function

num_left_cluster = 50 num_right_cluster = 50 start_gamma = 5e6; exponential = 15; smooth_cost = 1e5; num_iterations = 100; (gamma_head becomes Inf in the middle of the iterations; I also tried num_iter = 7 such that all gamma_head values are finite in the iterations, but the outputs from the two values are quite similar) num_runs = 1;

I computed the gradient prior file using the speedup_gradient code

HCP 500 subjects:

From example fsaverage6 data:

[rubykong]

@Matilda-Yxx Has helped resolve this issue through email. I will close this issue, for any relevant questions feel free to email xiaoxuan.427@gmail.com