Connectivity equal to 0 when running DSI Studio on ubuntu 18.04

[Giorgia Baron]

Good day,

I'm trying to run the following DSI studio command inside the matlab toolbox "Lesion Quantification Toolkit" from matlab:

'! dsi_studio --action=ana --source=/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/HCP_842/HCP842_1mm.fib.gz --tract=/Lesion_Quantification_Toolkit/Support_Tools/Tractography_Atlas/HCP_842/all_tracts_1mm.trk.gz --roi=/Lesion_Quantification_Toolkit/Support_Tools/Example_Lesions/FCS_026_A_lesion_111_fnirt_111MNI.nii --output=/Lesion_Quantification_Toolkit/Test4/test/Parcel_Disconnection/test_Yeo7100.trk.gz --connectivity=/Lesion_Quantification_Toolkit/Support_Tools/Parcellations/Schaefer_Yeo/Schaefer2018_100Parcels_7Networks_order_FSLMNI152_1mm.nii --connectivity_type=end --connectivity_threshold=0 --export=tdi'

While the same DSI Studio 2024 version successfully returns the connectivity matrix when executed on windows, it does not return the matrix on ubuntu 18.04, since the connectivity mat file is equal to zero. How can I solve this problem? Could it be related to the LD_LIBRARY_PATH of Linux?

Thank you,

Giorgia

[Frank Yeh]

Could you post the log output?

You may add direction (e.g. > log.txt) to the end of the command.

Frank

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[Frank Yeh]

- "While the same DSI Studio 2024 version successfully returns the connectivity matrix when executed on windows,"

Could you post the console output from Windows?

You may compare them and see what made the difference.

On Wed, Jun 12, 2024 at 9:25 AM Giorgia Baron <giorgia...@studenti.unipd.it> wrote:

Hi Frank,

thank your for your reply. I attached the log file.

Giorgia

[Giorgia Baron]

Hi Frank,

thank your for your reply. I attached the log file.

Giorgia

Il giorno mer 12 giu 2024 alle ore 15:11 Frank Yeh <fran...@gmail.com> ha scritto:

[Giorgia Baron]

I have also attached the log file for the Windows version. At the bottom of the file, you will find a copy of the command we used in the toolkit.

Thank you for your assistance.

Giorgia

[Frank Yeh]

I am sorry that I don't know much about your study approach.

I would suggest that you compare them to figure out the differences.

Best regards,

Frank

[Giorgia Baron]

Dear Frank,

the differences regard the following rows that are performed only for the Windows versions, even when the command lines are the same in both versions:

| | | | [0;33madd 5755 voxel(s) as a region with image size [0m: (182,218,182) resolution: 1 1 1  
| | | | [0;33madd 7143 voxel(s) as a region with image size [0m: (182,218,182) resolution: 1 1 1  
| | | | [0;33madd 6702 voxel(s) as a region with image size [0m: (182,218,182) resolution: 1 1 1  
| | | | [0;33madd 12608 voxel(s) as a region with image size [0m: (182,218,182) resolution: 1 1 1  
| | | | [0;33madd 7399 voxel(s) as a region with image size [0m: (182,218,182) resolution: 1 1 1  
| | | | [0;33madd 8251 voxel(s) as a region with image size [0m: (182,218,182) resolution: 1 1 1  
| | | | [0;33madd 7548 voxel(s) as a region with image size [0m: (182,218,182) resolution: 1 1 1  
| | | | [0;33madd 14834 voxel(s) as a region with image size [0m: (182,218,182) resolution: 1 1 1  
| | | | [0;33madd 8590 voxel(s) as a region with image size [0m: (182,218,182) resolution: 1 1 1  
| | | | [0;33madd 12085 voxel(s) as a region with image size [0m: (182,218,182) resolution: 1 1 1  
| | | | [0;33madd 4219 voxel(s) as a region with image size [0m: (182,218,182) resolution: 1 1 1  
| | | | [0;33madd 8885 voxel(s) as a region with image size [0m: (182,218,182) resolution: 1 1 1 

...

Giorgia

[Frank Yeh]

I took a quick check on both log files. They are all different everywhere.

I would suggest have a detailed check to make sure they are identical except for the GUI related output.

Best regards 

Frank

Giorgia Baron <giorgia...@studenti.unipd.it> 于 2024年6月13日周四 上午2:25写道：

[Frank Yeh]

You may need to update both versions to the latest version.

DSIStudio is updated frequently on the monthly to weekly basis.

Best regards 

Frank

Dear Frank,

We have reviewed both files and reran the Linux version using the same atlas as in the Windows version example (please see the attached log file). As observed, the software fails to locate the .txt label file in both instances. However, the Windows version continues with the connectivity estimation, while the Linux version does not produce this output. In both scenarios, we used the example scripts provided in the toolkit, along with the included example files, expecting it to generate some output files.

Thank you for your assistance.

Best regards,

Giorgia

[Giorgia Baron]

Dear Frank,

We have reviewed both files and reran the Linux version using the same atlas as in the Windows version example (please see the attached log file). As observed, the software fails to locate the .txt label file in both instances. However, the Windows version continues with the connectivity estimation, while the Linux version does not produce this output. In both scenarios, we used the example scripts provided in the toolkit, along with the included example files, expecting it to generate some output files.

Thank you for your assistance.

Best regards,

Giorgia