sh-4.2$ singularity exec -B /data /data/singularity-images/dsistudio_20221006.sif dsi_studio --action=atk --source=*fib.gz --thread_count=3 --trk_format=trk.gz --output=/data/TEST --track_id=Uncinate,Cingulum,Fornix
+ DSI Studio version: Chen"陳" command line
| DSI Studio version: Chen"陳"
| action=atk
| source=*fib.gz
| + run atk
| | searching *fib.gz
| | found 1 files.
| | track_id=Uncinate,Cingulum,Fornix
| | target tracks: Cingulum_Frontal_Parahippocampal_L Cingulum_Frontal_Parahippocampal_R Cingulum_Frontal_Parietal_L Cingulum_Frontal_Parietal_R Cingulum_Parahippocampal_Parietal_L Cingulum_Parahippocampal_Parietal_R Cingulum_Parahippocampal_L Cingulum_Parahippocampal_R Cingulum_Parolfactory_L Cingulum_Parolfactory_R Uncinate_Fasciculus_L Uncinate_Fasciculus_R Fornix_L Fornix_R
| | tolerance=22,26,30
| | track_voxel_ratio=2
| | yield_rate=1e-05
| | tip_iteration=48
| | export_stat=1
| | export_trk=1
| | overwrite=0
| | export_template_trk=0
| | check_ending=1
| | thread_count=3
| | trk_format=trk.gz
| | output=/data/TEST
| | + automatic fiber tracking
| | | + eddy0730_outlierfreedata
| | | | processing eddy0730_outlierfreedata
| | | | + tracking pathways
| | | | | + Cingulum_Frontal_Parahippocampal_L
| | | | | | + open FIB file
| | | | | | | + opening eddy0730_outlierfreedata.icbm152_adult.qsdr.1.3.R67.fib.gz
| | | | | | | |_421 ms
| | | | | | | + loading fiber and image data
| | | | | | | | + loading image volumes
| | | | | | | | |_44 ms
| | | | | | | | + initiating data
| | | | | | | | | matched template: /opt/dsi-studio/atlas/ICBM152_adult/ICBM152_adult.QA.nii.gz
| | | | | | | | |_1 ms
| | | | | | | |_45 ms
| | | | | | | FIB file loaded
| | | | | | |_467 ms
| | | | | | + loading ICBM152_adult.tt.gz
| | | | | | | + opening ICBM152_adult.tt.gz
| | | | | | | |_39 ms
| | | | | | |_60 ms
| | | | | | + opening ICBM152_adult.QA.nii.gz
| | | | | | |_1 ms
| | | | | | + reading image data
| | | | | | |_68 ms
| | | | | | + warping atlas tracks to subject space
| | | | | | |_21 ms
| | | | | | min_length(mm): 88.3862
| | | | | | max_length(mm): 298.679
| | | | | | + tracking Cingulum_Frontal_Parahippocampal_L
| | | | | | | + loading tractography atlas
| | | | | | | convert tolerance distance of 22 from ICBM mm to 14.6667 subject voxels
| | | | | | | creating seed region from tractography atlas
| | | | | | | region dimension: (104,126,90)
| | | | | | | region voxel size: 1.5 1.5 1.5
| | | | | | | region voxel count: 1688
| | | | | | | creating ROA region to limit tracking results
| | | | | | | apply left mask for Cingulum_Frontal_Parahippocampal_L
| | | | | | | yield rate (tract generated per seed): 0.00781569
| | | | | | | tract yield rate (tracts per second): 1126.99
| | | | | | | seed yield rate (seeds per second): 144195
| | | | | | | + save trajectories to eddy0730_outlierfreedata.Cingulum_Frontal_Parahippocampal_L.tt.gz
| | | | | | | | + compressing trajectories
| | | | | | | | |_6 ms
| | | | | | | | + saving file
| | | | | | | | |_57 ms
| | | | | | | |_64 ms
| | | | | | |_18.864 s
| | | | | | + export tracts statistics
| | | | | | | saving /data/TEST/Cingulum_Frontal_Parahippocampal_L/eddy0730_outlierfreedata.Cingulum_Frontal_Parahippocampal_L.stat.txt
| | | | | | | region dimension: (104,126,90)
| | | | | | | region voxel size: 1.5 1.5 1.5
| | | | | | | region voxel count: 70
| | | | | | | region dimension: (104,126,90)
| | | | | | | region voxel size: 1.5 1.5 1.5
| | | | | | | region voxel count: 344
| | | | | | | rdi loaded
| | | | | | | ad loaded
| | | | | | | t1w loaded
| | | | | | | dti_fa loaded
| | | | | | | iso loaded
| | | | | | | md loaded
| | | | | | | rd loaded
| | | | | | | nrdi06L loaded
| | | | | | | nrdi04L loaded
| | | | | | | nrdi02L loaded
| | | | | | |_351 ms
| | | | | |_19.879 s
| | | | | + Cingulum_Frontal_Parahippocampal_R
| | | | | | min_length(mm): 87.374
| | | | | | max_length(mm): 283.229
| | | | | | + tracking Cingulum_Frontal_Parahippocampal_R
| | | | | | | + loading tractography atlas
| | | | | | | convert tolerance distance of 22 from ICBM mm to 14.6667 subject voxels
| | | | | | | creating seed region from tractography atlas
| | | | | | | region dimension: (104,126,90)
| | | | | | | region voxel size: 1.5 1.5 1.5
| | | | | | | region voxel count: 1694
| | | | | | | creating ROA region to limit tracking results
| | | | | | | apply right mask for Cingulum_Frontal_Parahippocampal_R