Problem with connectivity output in CLI with --trk and --ana: --connectivity_value is not used/recognized.

[Oscar K]

I'm very new to connectomics, so it's probably a simple fix or a misunderstanding on my part, but I don't think that I've missed anything in the docs. I would really appreciate the help.

TL;DR:
I'm getting `--connectivity_value is not used/recognized.` when trying to calculate and output connectivity matrices for only one metric (count) using the CLI, either with --ana or --trk and either with `--connectivity_value` OR `--connectivity_output`.

Data: HCP-a from https://brain.labsolver.org/mds/data-hcp/lifespan.html ; I'm using the qsdr.fz files.

N.B.: Tracking works fine in the CLI and the connectivity works in the GUI.

System: Ubuntu 22.04.5 LTS
DSI-Studio: Ubuntu x86_64 (20.04+) (version for Ubuntu 22.04) both GPU and CPU versions tested.

Details:

Tracking works fine with the following command:

```
./dsi-studio/dsi_studio \
    --action=trk \
    --source="./HCA6002236.qsdr.fz" \
    --output="./output/HCA6002236/HCA6002236.tt.gz" \
    --track_voxel_ratio=4 \
    --thread_count=16
```

and adding `--connectivity=HCP-MMP` and `--connectivity_type=pass` generates both R2R and T2R .mat and .txt for all metrics, which both takes up alot of space (700 subjects) and takes time. Thus I want to add `--connectivity_value=count` and `--connectivity_output=matrix` as per the documentation. But either one of these gives the following error:
```
...
│  │  │  └──⏱1.50437m
│  │  └──⏱1.50437m
│  └──⏱1.51278m
└──⏱1.51278m
❗--connectivity_value is not used/recognized.
❗--connectivity_output is not used/recognized.
```

I've tried to isolate the connectivity and run it with `--action=ana` on the tracts directly, like so:

```bash
./dsi-studio/dsi_studio --action=ana \
--source="./HCA6002236.qsdr.fz" \
--tract="./output/HCA6002236/HCA6002236.tt.gz" \
--connectivity=HCP-MMP \
--connectivity_type=pass \
--connectivity_value=count \
--connectivity_output=matrix
```

But this gives the same error as above.

Full output:
```
$ ./dsi-studio/dsi_studio   --action=ana   --source="/media/[redacted]/neuro/HCP_test/HCA6002236.qsdr.fz"   --tract="./output/HCA6002236/HCA6002236.tt.gz"   --connectivity=HCP-MMP --connectivity_type=pass --connectivity_value=count --connectivity_output=matrix
DSI Studio (Yeh 2025, doi:10.1038/s41592-025-02762-8), the Hou "侯" version (Jan 21 2026, http://dsi-studio.labsolver.org)
action=ana
├──CUDA Driver Version: 12020 CUDA Run Time Version: 11080
│  ├──device count: 1
│  ├──device number: 0
│  ├──arch: 89
│  ├──device name: NVIDIA GeForce RTX 4060
│  ├──memory clock rate (KHz): 8501000
│  ├──memory bus width (bits): 128
│  ├──peak memory bandwidth (GB/s): 272.032
CPU/GPU computation enabled
┌──📟command line
├──thread_count=32
├──source=/media/[redacted]/neuro/HCP_test/HCA6002236.qsdr.fz
├──┬──📟run ana
│  ├──┬──📂opening /media/[redacted]/neuro/HCP_test/HCA6002236.qsdr.fz
│  │  ├──fib_ver: 202408
│  │  ├──dim: 106 133 106 vs: 1.5 1.5 1.5
│  │  ├──trans: -1.5 -0 0 79.5; -0 -1.5 0 81.5; -0 -0 1.5 -72; 0 0 0 1;
│  │  ├──is qsdr: yes
│  │  ├──mask voxels: 643869
│  │  ├──┬──📟loading image volumes
│  │  │  └──⏱11ms
│  │  ├──template: ICBM152_adult
│  │  ├──┬──📂open [redacted]/dsi-studio/atlas/human/human.QA.nii.gz
│  │  │  └──⏱0ms
│  │  ├──matched template (by image size): human
│  │  └──⏱51ms
│  ├──tract=./output/HCA6002236/HCA6002236.tt.gz
│  ├──┬──📂open ./output/HCA6002236/HCA6002236.tt.gz
│  │  ├──using index file for accelerated loading: ./output/HCA6002236/HCA6002236.tt.gz.idx
│  │  └──⏱383ms
│  ├──host space (mni): -1.5 -0 0 79.5; -0 -1.5 0 81.5; -0 -0 1.5 -72; 0 0 0 1;
│  ├──tractography space (native):
│  ├──-1.5 -0 0 79.5; -0 -1.5 0 81.5; -0 -0 1.5 -72; 0 0 0 1;
│  ├──A total of 1328588 tracks loaded
│  ├──a total of 1 tract file(s) loaded
│  ├──┬──📟post-tracking analysis
│  │  ├──┬──📟load all image volume
│  │  │  ├──dti_fa loaded
│  │  │  ├──rd loaded
│  │  │  ├──iso loaded
│  │  │  ├──rdi loaded
│  │  │  ├──nrdi02L loaded
│  │  │  ├──compute qir from qa and iso
│  │  │  ├──qir loaded
│  │  │  ├──connectivity=HCP-MMP
│  │  │  ├──┬──📂open [redacted]/dsi-studio/atlas/human/HCP-MMP.nii.gz
│  │  │  │  └──⏱16ms
│  │  │  ├──connectivity_type=pass
│  │  │  ├──┬──📟calculating connectivity matrix
│  │  │  │  ├──tract count: 1328588
│  │  │  │  ├──use_end_only: no
│  │  │  │  ├──atlas_name: HCP-MMP
│  │  │  │  ├──┬──📟calculating matrices
│  │  │  │  │  └──⏱1.0783m
│  │  │  │  └──⏱1.08863m
│  │  │  ├──💾saving region-to-region connectome
│  │  │  ├──💾saving ./output/HCA6002236/HCA6002236.tt.gz.HCP-MMP.number_of_tracts.connectivity.mat
│  │  │  ├──💾saving ./output/HCA6002236/HCA6002236.tt.gz.HCP-MMP.number_of_tracts.connectogram.txt
│  │  │  ├──💾saving ./output/HCA6002236/HCA6002236.tt.gz.HCP-

[ ... ]

MMP.intersect_ratio.connectivity.mat

│  │  │  ├──💾saving ./output/HCA6002236/HCA6002236.tt.gz.HCP-MMP.intersect_ratio.connectogram.txt
│  │  │  ├──💾saving ./output/HCA6002236/HCA6002236.tt.gz.HCP-MMP.intersect_ratio.network_measures.txt
│  │  │  ├──💾saving ./output/HCA6002236/HCA6002236.tt.gz.HCP-MMP.intersect_volume.connectivity.mat
│  │  │  ├──💾saving ./output/HCA6002236/HCA6002236.tt.gz.HCP-MMP.intersect_volume.connectogram.txt
│  │  │  ├──💾saving ./output/HCA6002236/HCA6002236.tt.gz.HCP-MMP.intersect_volume.network_measures.txt
│  │  │  ├──generating tract-to-region connectome
│  │  │  ├──💾saving ./output/HCA6002236/HCA6002236.tt.gz.HCP-MMP.tract2region.txt
│  │  │  └──⏱1.50728m
│  │  └──⏱1.50728m
│  └──⏱1.516m
└──⏱1.516m
❗--connectivity_value is not used/recognized.
❗--connectivity_output is not used/recognized.

```

[Frank Yeh]

Sorry for the confusion. The document needs to be updated (will do so soon).
The latest version now outputs all values because it takes similar
time to output all. Thus these two options are ignored.
I will review the code to reinstate the function at my best.

Best regards,
Frank

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[Frank Yeh]

I updated DSI Studio to reinstate --connectivity_value and --connectivity_output
The documentation is also updated at
https://dsi-studio.labsolver.org/doc/cli_t3.html

Thanks again for reporting this issue, and sorry for the confusion.
The new build is under way and should be ready in one hour or two.

Best regards,
Frank