┌──📟DSI Studio (Yeh 2025, doi:10.1038/s41592-025-02762-8), the Hou "侯" version (Jul 9 2026, http://dsi-studio.labsolver.org)
├──CUDA Driver Version: 13020 CUDA Run Time Version: 12080
│ ├──device count: 1
│ ├──device number: 0
│ ├──arch: 86
│ ├──device name: NVIDIA GeForce RTX 3060 Laptop GPU
│ ├──memory clock rate (KHz): 7001000
│ ├──memory bus width (bits): 192
│ ├──peak memory bandwidth (GB/s): 336.048
├──Enable multi-thread CPU/GPU computation
├──┬──📂open sub-AT7881_ses-01_space-T2w_desc-preproc_dwi.qsdr.fz
│ ├──fib_ver: 202504 dim: 150 213 90 vs: 0.075 0.075 0.075 qsdr: yes
│ ├──trans: -0.075 0 0 5.6375; 0 -0.075 0 6.6775; 0 0 0.075 -2.3875; 0 0 0 1;
│ ├──mask voxels: 1244865
│ ├──┬──📟loading image volumes
│ │ ├──fiber metrics: qa,qir
│ │ ├──voxel metrics: vol,dti_fa,rd,iso,rdi,nrdi02L,nrdi04L
│ │ └──⏱75ms
│ ├──template: mouse
│ └──⏱172ms
├──┬──📟initializing tracking GUI
│ ├──create GUI objects
│ ├──prepare template and atlases
│ ├──initialize slices
│ ├──connect signal and slots
│ ├──begin visualization
│ ├──GUI initialization complete
│ └──⏱1s85ms
├──┬──📟initializing OpenGL
│ ├──version: 4.6.0 NVIDIA 596.49
│ ├──vendor: NVIDIA Corporation
│ ├──renderer: NVIDIA GeForce RTX 3060 Laptop GPU/PCIe/SSE2
│ └──⏱0ms
├──loading tractography atlas label from C:/Users/adamr/Downloads/dsi_studio_win/dsi_studio_win\tract\mouse.txt
├──┬──📟loading symmetric tractography atlas
│ ├──┬──📂openC:/Users/adamr/Downloads/dsi_studio_win/dsi_studio_win\tract\mouse.tt.gz
│ │ └──⏱119ms
│ ├──cluster information loaded
│ ├──host space (mni): -0.075 0 0 5.6375; 0 -0.075 0 6.6775; 0 0 0.075 -2.3875; 0 0 0 1;
│ ├──tractography space (mni):
│ ├──-0.1 0 0 5.6375; 0 -0.1 0 6.6775; 0 0 0.1 -2.3875; 0 0 0 1;
│ ├──applying linear transform, condition: loading tract to a different srow
│ ├──from space: -0.1 0 0 5.6375; 0 -0.1 0 6.6775; 0 0 0.1 -2.3875; 0 0 0 1;
│ ├──to space: -0.075 0 0 5.6375; 0 -0.075 0 6.6775; 0 0 0.075 -2.3875; 0 0 0 1;
│ ├──┬──📟apply transform to tracts
│ │ ├──1.33333 0 0 0; 0 1.33333 0 0; 0 0 1.33333 -1.90735e-06; 0 0 0 1;
│ │ └──⏱7ms
│ ├──┬──📟warping template tracts to subject space
│ │ └──⏱9ms
│ └──⏱173ms
├──threshold: 0
├──default_otsu: 0.6
├──cull_cos_angle: 1
├──step_size: 0
├──smooth_fraction: 0
├──min_length: 1.5
├──max_length: 10
├──max_tract_count: 0
├──max_seed_count: 0
├──track_voxel_ratio: 0.5625
├──tracking_method: 0
├──check_ending: 0
├──reserved6(random_seed DEPRECATED): 0
├──tip_iteration: 4
├──dt_threshold: 0.2
├──random_seed: 0
├──reserved3: 0
├──reserved4: 0
├──┬──📟initiating fiber tracking
│ ├──tracking in threads
│ │ [thread 34804]📟loading atlas regions
│ │ [thread 34804]convert tolerance distance of 1.20 from ICBM mm to 16.00 subject voxels
│ └──⏱4ms
│ [thread 34804]📟create limiting mask
│ [thread 34804]apply left mask for CingulumL
│ [thread 34804]📟create limiting/seeding/not end regions
│ [thread 34804]A limiting region was placed at track tolerance region (85,96,61).
│ [thread 34804]A seeding region was placed at CingulumL (85,96,61).
│ [thread 34804]📟configure tract targets
│ [thread 34804]for tract-to-voxel ratio of 0.5625, the maximum tract counts are set to 42077
├──┬──📟trimming
│ ├──433 tracts removed by trimming.
│ ├──tract count after trimming: 41644
│ └──⏱93ms
##############################################################
On the CLI:
apptainer exec /groups/adamraikes/singularity_images/dsistudio_2026-07-15_tls.sif dsi_studio --action=atk --source=*.fz --track_id=Cingulum --template=6 --tip_iteration=4 --check_ending=0
DSI Studio (Yeh 2025, doi:10.1038/s41592-025-02762-8), the Hou "侯" version (Jul 9 2026, http://dsi-studio.labsolver.org)
action=atk
Enable multi-thread CPU computation
┌──📟command line
├──┬──📟run atk
│ ├──source=*.fz
│ ├──*.fz: 1 file(s) specified by *.fz
│ ├──trk_format=tt.gz
│ ├──yield_rate=1e-05
│ ├──overwrite=0
│ ├──template 0:human 1:human-neonate 2:chimpanzee 3:rhesus 4:marmoset 5:rat 6:mouse
│ ├──template=6
│ ├──loading tractography atlas label from /opt/dsi-studio/tract/mouse.txt
│ ├──available track_ids in current template: Association_CingulumL,Association_CingulumR,Association_SuperiorLongitudinalFasciculusL,Association_SuperiorLongitudinalFasciculusR,Commissure_AnteriorCommissure,Commissure_AnteriorCommissure_Frontal,Commissure_AnteriorCommissure_Occipital,Commissure_AnteriorCommissure_Temporal,Commissure_CorpusCallosum,Commissure_CorpusCallosum_Body,Commissure_CorpusCallosum_ForcepsMajor,Commissure_CorpusCallosum_ForcepsMinor,Commissure_Hippocampal,Commissure_Thalamic,ProjectionBasalGanglia_FasciculusRetroflexusL,ProjectionBasalGanglia_FasciculusRetroflexusR,ProjectionBasalGanglia_FornixL,ProjectionBasalGanglia_FornixR,ProjectionBasalGanglia_MammilloThalamicTractL,ProjectionBasalGanglia_MammilloThalamicTractR,ProjectionBasalGanglia_OlfactoryTractL,ProjectionBasalGanglia_OlfactoryTractL_Acccessory,ProjectionBasalGanglia_OlfactoryTractL_Main,ProjectionBasalGanglia_OlfactoryTractR,ProjectionBasalGanglia_OlfactoryTractR_Acccessory,ProjectionBasalGanglia_OlfactoryTractR_Main,ProjectionBasalGanglia_OpticRadiationL,ProjectionBasalGanglia_OpticRadiationR,ProjectionBasalGanglia_OpticTractL,ProjectionBasalGanglia_OpticTractR,ProjectionBasalGanglia_PAGL,ProjectionBasalGanglia_PAGR,ProjectionBasalGanglia_StriaMedullarisL,ProjectionBasalGanglia_StriaMedullarisR,ProjectionBasalGanglia_StriaTerminalisL,ProjectionBasalGanglia_StriaTerminalisL,ProjectionBasalGanglia_TectoThalamicL,ProjectionBasalGanglia_TectoThalamicR,ProjectionBrainstem_CorticospinalTractL,ProjectionBrainstem_CorticospinalTractR,ProjectionBrainstem_ReticularTractL,ProjectionBrainstem_ReticularTractR,ProjectionBrainstem_TrigeminalTractL,ProjectionBrainstem_TrigeminalTractR
│ ├──track_id=Cingulum
│ ├──selected tracts: Association_CingulumL,Association_CingulumR
│ ├──┬──📟automatic fiber tracking
│ │ ├──processing sub-AT7881_ses-01_space-T2w_desc-preproc_dwi.qsdr.fz
│ │ ├──┬──📟tracking pathways
│ │ │ ├──tracking Association_CingulumL
│ │ │ ├──┬──📂open/xdisk/adamraikes/p3/derivatives/dmriprep_2026_v4/sub-AT7881/ses-01/dwi/tmp/sub-AT7881_ses-01_space-T2w_desc-preproc_dwi.qsdr.fz
│ │ │ │ ├──fib_ver: 202504 dim: 150 213 90 vs: 0.075 0.075 0.075 qsdr: yes
│ │ │ │ ├──trans: -0.075 0 0 5.6375; 0 -0.075 0 6.6775; 0 0 0.075 -2.3875; 0 0 0 1;
│ │ │ │ ├──mask voxels: 1244865
│ │ │ │ ├──┬──📟loading image volumes
│ │ │ │ │ ├──fiber metrics: qa,qir
│ │ │ │ │ ├──voxel metrics: vol,dti_fa,rd,iso,rdi,nrdi02L,nrdi04L
│ │ │ │ │ └──⏱67ms
│ │ │ │ ├──template: mouse
│ │ │ │ └──⏱189ms
│ │ │ ├──template 0:human 1:human-neonate 2:chimpanzee 3:rhesus 4:marmoset 5:rat 6:mouse
│ │ │ ├──template=mouse
│ │ │ ├──tolerance=1.2,1.275,1.35
│ │ │ ├──loading tractography atlas label from /opt/dsi-studio/tract/mouse.txt
│ │ │ ├──┬──📟loading symmetric tractography atlas
│ │ │ │ ├──┬──📂open/opt/dsi-studio/tract/mouse.tt.gz
│ │ │ │ │ └──⏱165ms
│ │ │ │ ├──cluster information loaded
│ │ │ │ ├──host space (mni): -0.075 0 0 5.6375; 0 -0.075 0 6.6775; 0 0 0.075 -2.3875; 0 0 0 1;
│ │ │ │ ├──tractography space (mni):
│ │ │ │ ├──-0.1 0 0 5.6375; 0 -0.1 0 6.6775; 0 0 0.1 -2.3875; 0 0 0 1;
│ │ │ │ ├──applying linear transform, condition: loading tract to a different srow
│ │ │ │ ├──from space: -0.1 0 0 5.6375; 0 -0.1 0 6.6775; 0 0 0.1 -2.3875; 0 0 0 1;
│ │ │ │ ├──to space: -0.075 0 0 5.6375; 0 -0.075 0 6.6775; 0 0 0.075 -2.3875; 0 0 0 1;
│ │ │ │ ├──┬──📟apply transform to tracts
│ │ │ │ │ ├──1.33333 0 0 0; 0 1.33333 0 0; 0 0 1.33333 -1.90735e-06; 0 0 0 1;
│ │ │ │ │ └──⏱10ms
│ │ │ │ ├──┬──📟warping template tracts to subject space
│ │ │ │ │ └──⏱43ms
│ │ │ │ └──⏱266ms
│ │ │ ├──otsu_threshold=0.6
│ │ │ ├──fa_threshold=0
│ │ │ ├──turning_angle=0
│ │ │ ├──step_size=0
│ │ │ ├──smoothing=0
│ │ │ ├──tip_iteration=4
│ │ │ ├──check_ending=0
│ │ │ ├──track_voxel_ratio=0.5625
│ │ │ ├──use_roi=1
│ │ │ ├──min_length(mm): 0.157603
│ │ │ ├──max_length(mm): 0.791175
│ │ │ ├──┬──📟tracking Association_CingulumL
│ │ │ │ ├──tracking in threads
│ │ │ │ │ [thread 140449557755648]📟loading atlas regions
│ │ │ │ │ [thread 140449557755648]convert tolerance distance of 1.20 from ICBM mm to 16.00 subject voxels
│ │ │ │ │ [thread 140449557755648]📟create limiting mask
│ │ │ │ │ [thread 140449557755648]apply left mask for Association_CingulumL
│ │ │ │ │ [thread 140449557755648]📟create limiting/seeding/not end regions
│ │ │ │ │ [thread 140449557755648]A limiting region was placed at track tolerance region (85,96,61).
│ │ │ │ │ [thread 140449557755648]A seeding region was placed at Association_CingulumL (85,96,61).
│ │ │ │ │ [thread 140449557755648]📟configure tract targets
│ │ │ │ │ [thread 140449557755648]for tract-to-voxel ratio of 0.5625, the maximum tract counts are set to 42077
│ │ │ │ ├──low yield rate, adjusting tolerance and restart...
│ │ │ │ ├──total tract generated: 0
│ │ │ │ ├──yield rate (tract generated per seed): 0
│ │ │ │ ├──tract yield rate (tracts per second): 0
│ │ │ │ ├──seed yield rate (seeds per second): 265149
│ │ │ │ └──⏱3s773ms
│ │ │ ├──otsu_threshold=0.6
│ │ │ ├──fa_threshold=0
│ │ │ ├──turning_angle=0
│ │ │ ├──step_size=0
│ │ │ ├──smoothing=0
│ │ │ ├──track_voxel_ratio=0.5625
│ │ │ ├──use_roi=1
│ │ │ ├──min_length(mm): 0.146353
│ │ │ ├──max_length(mm): 0.802425
│ │ │ ├──┬──📟tracking Association_CingulumL
│ │ │ │ ├──tracking in threads
│ │ │ │ │ [thread 140449591326464]📟loading atlas regions
│ │ │ │ │ [thread 140449591326464]convert tolerance distance of 1.28 from ICBM mm to 17.00 subject voxels
│ │ │ │ │ [thread 140449591326464]📟create limiting mask
│ │ │ │ │ [thread 140449591326464]apply left mask for Association_CingulumL
│ │ │ │ │ [thread 140449591326464]📟create limiting/seeding/not end regions
│ │ │ │ │ [thread 140449591326464]A limiting region was placed at track tolerance region (85,96,61).
│ │ │ │ │ [thread 140449591326464]A seeding region was placed at Association_CingulumL (85,95,61).
│ │ │ │ │ [thread 140449591326464]📟configure tract targets
│ │ │ │ │ [thread 140449591326464]for tract-to-voxel ratio of 0.5625, the maximum tract counts are set to 46046
│ │ │ │ ├──low yield rate, adjusting tolerance and restart...
│ │ │ │ ├──total tract generated: 0
│ │ │ │ ├──yield rate (tract generated per seed): 0
│ │ │ │ ├──tract yield rate (tracts per second): 0
│ │ │ │ ├──seed yield rate (seeds per second): 218847
│ │ │ │ └──⏱4s571ms
│ │ │ ├──otsu_threshold=0.6
│ │ │ ├──fa_threshold=0
│ │ │ ├──turning_angle=0
│ │ │ ├──step_size=0
│ │ │ ├──smoothing=0
│ │ │ ├──track_voxel_ratio=0.5625
│ │ │ ├──use_roi=1
│ │ │ ├──min_length(mm): 0.135103
│ │ │ ├──max_length(mm): 0.813675
│ │ │ ├──┬──📟tracking Association_CingulumL
│ │ │ │ ├──tracking in threads
│ │ │ │ │ [thread 140449557755648]📟loading atlas regions
│ │ │ │ │ [thread 140449557755648]convert tolerance distance of 1.35 from ICBM mm to 18.00 subject voxels
│ │ │ │ │ [thread 140449557755648]📟create limiting mask
│ │ │ │ │ [thread 140449557755648]apply left mask for Association_CingulumL
│ │ │ │ │ [thread 140449557755648]📟create limiting/seeding/not end regions
│ │ │ │ │ [thread 140449557755648]A limiting region was placed at track tolerance region (86,96,60).
│ │ │ │ │ [thread 140449557755648]A seeding region was placed at Association_CingulumL (86,95,60).
│ │ │ │ │ [thread 140449557755648]📟configure tract targets
│ │ │ │ │ [thread 140449557755648]for tract-to-voxel ratio of 0.5625, the maximum tract counts are set to 50270
│ │ │ │ ├──low yield rate, adjusting tolerance and restart...
│ │ │ │ ├──total tract generated: 0
│ │ │ │ ├──yield rate (tract generated per seed): 0
│ │ │ │ ├──tract yield rate (tracts per second): 0
│ │ │ │ ├──seed yield rate (seeds per second): 178529
│ │ │ │ └──⏱5s608ms
│ │ │ ├──❗ no tracking result generated for Association_CingulumL
############################################################
Running as action=trk in GUI console:
├──┬──📟command line
│ ├──action=trk
│ ├──source=sub-AT7881_ses-01_space-T2w_desc-preproc_dwi.qsdr.fz
│ ├──┬──📟run trk
│ │ ├──┬──📂opensub-AT7881_ses-01_space-T2w_desc-preproc_dwi.qsdr.fz
│ │ │ ├──fib_ver: 202504 dim: 150 213 90 vs: 0.075 0.075 0.075 qsdr: yes
│ │ │ ├──trans: -0.075 0 0 5.6375; 0 -0.075 0 6.6775; 0 0 0.075 -2.3875; 0 0 0 1;
│ │ │ ├──mask voxels: 1244865
│ │ │ ├──┬──📟loading image volumes
│ │ │ │ ├──fiber metrics: qa,qir
│ │ │ │ ├──voxel metrics: vol,dti_fa,rd,iso,rdi,nrdi02L,nrdi04L
│ │ │ │ └──⏱67ms
│ │ │ ├──template: mouse
│ │ │ └──⏱152ms
│ │ ├──threshold_index=qa
│ │ ├──template 0:human 1:human-neonate 2:chimpanzee 3:rhesus 4:marmoset 5:rat 6:mouse
│ │ ├──template=6
│ │ ├──┬──📟tracking parameters:
│ │ │ ├──otsu_threshold=0.6
│ │ │ ├──fa_threshold=0
│ │ │ ├──dt_threshold=0
│ │ │ ├──turning_angle=0
│ │ │ ├──step_size=0
│ │ │ ├──smoothing=0
│ │ │ ├──min_length=1.5
│ │ │ ├──max_length=10
│ │ │ ├──track_voxel_ratio=0.5625
│ │ │ ├──random_seed=0
│ │ │ ├──method=0
│ │ │ ├──check_ending=0
│ │ │ ├──tip_iteration=4
│ │ │ └──⏱0ms
│ │ ├──┬──📟setting up regions
│ │ │ ├──Consider using action atk for automatic fiber tracking
│ │ │ ├──loading tractography atlas label from C:/Users/adamr/Downloads/dsi_studio_win/dsi_studio_win\tract\mouse.txt
│ │ │ ├──┬──📟loading symmetric tractography atlas
│ │ │ │ ├──┬──📂openC:/Users/adamr/Downloads/dsi_studio_win/dsi_studio_win\tract\mouse.tt.gz
│ │ │ │ │ └──⏱145ms
│ │ │ │ ├──cluster information loaded
│ │ │ │ ├──host space (mni): -0.075 0 0 5.6375; 0 -0.075 0 6.6775; 0 0 0.075 -2.3875; 0 0 0 1;
│ │ │ │ ├──tractography space (mni):
│ │ │ │ ├──-0.1 0 0 5.6375; 0 -0.1 0 6.6775; 0 0 0.1 -2.3875; 0 0 0 1;
│ │ │ │ ├──applying linear transform, condition: loading tract to a different srow
│ │ │ │ ├──from space: -0.1 0 0 5.6375; 0 -0.1 0 6.6775; 0 0 0.1 -2.3875; 0 0 0 1;
│ │ │ │ ├──to space: -0.075 0 0 5.6375; 0 -0.075 0 6.6775; 0 0 0.075 -2.3875; 0 0 0 1;
│ │ │ │ ├──┬──📟apply transform to tracts
│ │ │ │ │ ├──1.33333 0 0 0; 0 1.33333 0 0; 0 0 1.33333 -1.90735e-06; 0 0 0 1;
│ │ │ │ │ └──⏱7ms
│ │ │ │ ├──┬──📟warping template tracts to subject space
│ │ │ │ │ └──⏱9ms
│ │ │ │ └──⏱207ms
│ │ │ ├──track_id=CingulumL
│ │ │ ├──use_roi=1
│ │ │ ├──tolerance=1.2
│ │ │ └──⏱207ms
│ │ ├──┬──📟fiber tracking
│ │ │ ├──┬──📟loading atlas regions
│ │ │ │ ├──convert tolerance distance of 1.20 from ICBM mm to 16.00 subject voxels
│ │ │ │ ├──┬──📟create limiting mask
│ │ │ │ │ ├──apply left mask for CingulumL
│ │ │ │ │ ├──┬──📟create limiting/seeding/not end regions
│ │ │ │ │ │ ├──A limiting region was placed at track tolerance region (85,96,61).
│ │ │ │ │ │ ├──A seeding region was placed at CingulumL (85,96,61).
│ │ │ │ │ │ └──⏱68ms
│ │ │ │ │ └──⏱86ms
│ │ │ │ ├──┬──📟configure tract targets
│ │ │ │ │ └──⏱1s215ms
│ │ │ │ └──⏱1s308ms
│ │ │ ├──for tract-to-voxel ratio of 0.5625, the maximum tract counts are set to 42077
│ │ │ └──⏱1m10s177ms
│ │ ├──┬──📟trimming
│ │ │ ├──414 tracts removed by trimming.
│ │ │ ├──tract count after trimming: 41663
│ │ │ └──⏱141ms
│ │ ├──41663 tracts are generated using 67342485 seeds.
│ │ ├──┬──📟post-tracking analysis
│ │ │ ├──delete_repeat=0.5
│ │ │ ├──repeated tracks with distance smaller than 0.5 voxel distance are deleted
│ │ │ ├──┬──📟delete repeated tracts
│ │ │ │ └──⏱1s56ms
│ │ │ ├──tract count after removing repeated tracts: 5494
│ │ │ ├──output=sub-AT7881_ses-01_Association_CingulumL.tt.gz
│ │ │ ├──💾save 5494 tracts to "sub-AT7881_ses-01_Association_CingulumL.tt.gz"
│ │ │ ├──dim:150 213 90 vs:0.075 0.075 0.075
│ │ │ ├──trans:-0.075 0 0 5.6375; 0 -0.075 0 6.6775; 0 0 0.075 -2.3875; 0 0 0 1;
│ │ │ ├──┬──💾savingsub-AT7881_ses-01_Association_CingulumL.tt.gz
│ │ │ │ ├──┬──📟compressing trajectories
│ │ │ │ │ └──⏱4ms
│ │ │ │ └──⏱104ms
│ │ │ └──⏱1s161ms
│ │ └──⏱1m11s928ms
│ └──⏱1m11s928ms
Hi Adam,
Thank you for the detailed log. From the log, the GUI is not only doing a generic tracking call. It first loads the mouse tractography atlas, applies the atlas-to-subject transform, creates the limiting mask, applies the left mask for CingulumL, tracks with the AutoTrack settings, and then removes repeated tracts.
One thing to note is that the final output in the log appears to be 5,494 tracts after removing repeated tracts:
removing repeated tracts: 5494
output=sub-AT7881_ses-01_Association_CingulumL.tt.gz
So if the CLI action=trk gives around 5k streamlines with the same final tract shape, it may actually be matching the final saved GUI output. The larger number you saw in the GUI may be the intermediate/generated streamline count before post-processing or duplicate removal.
The difference between action=atk and action=trk may come from the additional AutoTrack atlas/limiting-mask steps and tract-specific settings. The GUI AutoTrack uses the tract atlas and applies tract-specific masks/tolerance, whereas a minimal CLI command may not reproduce all of those internal steps unless the same tract name, atlas, tolerance, and tracking parameters are used.
I would suggest using the command history/console output from the successful GUI run as the starting point. If possible, please send me the exact action=atk and action=trk commands you used, and I can check which parameter is missing. The key is to reproduce the tract-specific limiting mask and atlas transformation, not only the generic tracking parameters.
Best,
Frank
##############################################################
On the CLI:
apptainer exec /groups/adamraikes/singularity_images/dsistudio_2026-07-15_tls.sif dsi_studio --action=atk --source=.fz --track_id=Cingulum --template=6 --tip_iteration=4 --check_ending=0
DSI Studio (Yeh 2025, doi:10.1038/s41592-025-02762-8), the Hou “侯” version (Jul 9 2026, http://dsi-studio.labsolver.org)
action=atk
Enable multi-thread CPU computation
┌──📟command line
├──┬──📟run atk
│ ├──source=.fz
│ │ │ │ ├──low yield rate, adjusting tolerance and restart…
│ │ │ │ ├──low yield rate, adjusting tolerance and restart…
│ │ │ │ ├──low yield rate, adjusting tolerance and restart…
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