Problem reading region in command line tractography

[viktor.do...@hotmail.com]

Dear Frank,

When I try to use command line tractography using the following command:

dsi_studio --action=trk --source=..\Data\SRCFiles\model.src.gz.021.dti.fib.gz --seed=..\Data\GMROIs\GM-ROI-ctx-lh-bankssts.nii.gz --seed_count=10000 --parameter_id=CDCCCC3D9A99193FF304353Fba4ba03FbA04b096431027da0101dba --output=..\Data\OutputFiles\GM-ROI-ctx-lh-bankssts.trk.gz --export=stat

I get the following error:

read region from ..\Data\GMROIs\Baseline\BO-BO\GM-ROI-ctx-lh-bankssts.nii.gz

Searching ..\Data\GMROIs\Baseline\BO-BO\GM-ROI-ctx-lh-bankssts.nii.gz from the atlas pool...

Load ..\Data\GMROIs\Baseline\BO-BO\GM-ROI-ctx-lh-bankssts.nii.gz failed. Cannot find file in C:/Users/CSIT/Desktop/ViktorD/dsi_studio_64/atlas/..\Data\GMROIs\Baseline\BO-BO\GM-ROI-ctx-lh-bankssts.nii.gz.nii.gz

..\Data\GMROIs\Baseline\BO-BO\GM-ROI-ctx-lh-bankssts.nii.gz does not exist. terminating...

Warning: --output is not used. Please check command line syntax.

Warning: --export is not used. Please check command line syntax.

The same command doesn't give any errors and works properly on another computer, with every part of the file system being the same in both computers. Do you have any ideas about what could cause the problem and how to fix it? 

Thank you in advance for your time.

Best regards,

Viktor

[Fang-Cheng Yeh]

It seems that DSI Studio cannot read " ..\Data\GMROIs\Baseline\BO-BO\GM-ROI-ctx-lh-bankssts.nii.gz"

You may need to check whether you have read access or whether the directories and filename have a typo.

Best regards,

Frank

--
You received this message because you are subscribed to the Google Groups "DSI Studio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to dsi-studio+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/0a9335fa-d26a-4a33-8478-74a170eccf95%40googlegroups.com.

[Daniel]

dsi_studio.app/Contents/MacOS/dsi_studio --action=ana \

--source=./dsi_studio.app/Contents/MacOS/atlas/human/human.fz \

--tract=all_tracts.tt.gz \

--roi=lesion_symptom_mapping/mni_lesion_mni.nii.gz \

--output=lesion_symptom_mapping/test_disconnectome \

--export=tdi

DSI Studio version: Hou "侯" Jul 16 2025

┌──📟command line

├──action=ana

├──thread_count=8

├──source=./dsi_studio.app/Contents/MacOS/atlas/human/human.fz

├──┬──📟run 

│  ├──┬──📂opening ./dsi_studio.app/Contents/MacOS/atlas/human/human.fz

│  │  ├──fib_ver: 0

│  │  ├──dim: 80 100 80 vs: 2 2 2 

│  │  ├──trans: -2 0 0 79.5; 0 -2 0 81.5; 0 0 2 -72; 0 0 0 1; 

│  │  ├──is qsdr: yes

│  │  ├──mask voxels: 275710

│  │  ├──┬──📟loading image volumes

│  │  │  └──⏱3ms

│  │  ├──matched template (by image size): human

│  │  └──⏱10ms

│  ├──roi=lesion_symptom_mapping/mni_lesion_mni.nii.gz

│  ├──load volume from lesion_symptom_mapping/mni_lesion_mni.nii.gz

│  ├──┬──📂opening file 

│  │  ├──mni_lesion_mni loaded as single ROI file

│  │  ├──FIB file size: 80 100 80 vs: 2 2 2  mni space

│  │  ├──mni_lesion_mni size: 182 218 182 vs: 1 1 1  not mni space (if mni space, add '.mni.' in file name)

│  │  ├──mni_lesion_mni has a different dimension from the FIB file. need transformation or warping.

│  │  ├──assume mni_lesion_mni is in the mni space (likely wrong. need to check).

│  │  ├──applying mni_lesion_mni's header srow matrix to align.

│  │  └──⏱37ms

│  ├──An ROI was placed at lesion_symptom_mapping/mni_lesion_mni.nii.gz (70,55,60).

│  ├──tract=all_tracts.tt.gz

│  ├──┬──📂opening all_tracts.tt.gz

│  │  └──⏱17ms

│  ├──host space (mni): -2 0 0 79.5; 0 -2 0 81.5; 0 0 2 -72; 0 0 0 1; 

│  ├──tractography space (native): 

│  ├──-2 0 0 79.5; 0 -2 0 81.5; 0 0 2 -72; 0 0 0 1; 

│  ├──A total of 20932 tracks loaded

│  ├──filtering tracts using roi/roa/end regions.

│  ├──remaining tract count: 1476

│  ├──a total of 1 tract file(s) loaded

│  ├──┬──📟post-tracking analysis

│  │  ├──output=lesion_symptom_mapping/test_disconnectome

│  │  ├──trk_format=tt.gz

│  │  ├──💾save tracts to lesion_symptom_mapping/test_disconnectome.tt.gz

│  │  ├──dim:80 100 80

│  │  ├──vs:2 2 2 

│  │  ├──trans:-2 0 0 79.5; 0 -2 0 81.5; 0 0 2 -72; 0 0 0 1; 

│  │  ├──┬──💾saving 

│  │  │  ├──┬──📟compressing trajectories

│  │  │  │  └──⏱0ms

│  │  │  └──⏱16ms

│  │  ├──export=tdi

│  │  ├──calculating TDI at x1 resolution

│  │  ├──TDI dimension: 80 100 80

│  │  ├──TDI voxel size: 2 2 2 

│  │  ├──💾saving lesion_symptom_mapping/test_disconnectome.tt.gz.tdi.nii.gz

│  │  └──⏱31ms

│  └──⏱105ms

└──⏱108ms

similar issue here.