I am using SIFT filtering on my tractogram output as such
tcksift my_track.tck wm_norm.mif my_track_sift.tck -term_number 50000000
I had previously generated my tractogram as such
tckgen wm_norm.mif my_track.tck -select 55000000 -cutoff 0.1
I am using a 55 million tractogram as input, to generate SIFT output with 50 million tracts
My error is
tcksift: [WARNING] existing output files will be overwritten tcksift: [100%] Creating homogeneous processing mask tcksift: [100%] segmenting FODs tcksift: [100%] mapping tracks to image tcksift: [WARNING] Only 1 tracks read from input track file; expected 50783078 tcksift: [ERROR] Filtering failed; desired number of filtered streamlines is greater than or equal to the size of the input dataset
I have read your previous discussion [HCP connectome tutorial] where there was a similar issue with SIFT (HCP connectome tutorial).
But the problem was, there was not enough tracks generated with
As suggested in the discussion, I have used tckinfo to check my tckgen output, given as
count: 55000000 downsample_factor: 2 fod_power: 0.333333343 init_threshold: 0.100000001 lmax: 8 max_angle: 22.5 max_num_seeds: 55000000000 max_num_tracks: 55000000 max_seed_attempts: 1000 max_trials: 1000 method: iFOD2 mrtrix_version: 3.0_RC2-7-g4ed6d5ef output_step_size: 0.100000001 rk4: 0 samples_per_step: 3 sh_precomputed: 1 source: wm_norm.mif step_size: 0.1 stop_on_all_include: 0 threshold: 0.1 timestamp: 1504146712.505079031 total_count: 60381056 unidirectional: 0
Under count I can see that I have 55 million tracks reported
I am not sure what is causing this. But I am very suspicious of the warning message which states
only 1 track read from input track file. Could this be an issue ? What is the reason for it ? Is this what is causing the filtering to fail ?