questions from a beginner

F.B.

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Feb 16, 2021, 2:51:25 PM2/16/21

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Hi Frank,

Happy Lunar New Year !

I am completely new to DSI Studio, a powerful and amazing tool for tractography.

As a beginner, I encountered some problems when getting familiar with the tool. Your help would be deeply appreciated.

Q1. FIB files could not be loaded

I downloaded the latest version--Feb.3,2021 build.

I installed DSI Studio on my 64-bit laptop with Windows 7 + Microsoft Visual C++ 2012 Redistributable(X64). I could create the SRC file and FIB file , and do fiber tracking on the FIB file.

However, after I installed DSI Studio(same version) on my 64-bit desktop PC with Windows 7, DSI Studio could not start to run due to missing msvcp140.dll and vcruntime140.dll. I copied both of the .dll files from my laptop and installed them on my desktop PC. DSI Studio started then. But I could not load any FIB files to do fiber tracking(Step T3) because the window of fiber tracking could not be displayed. DSI Studio was not responding, without any error messages. I then installed Microsoft Visual C++ 2013 Redistributable(X64) (from the link on DSI Studio download page) . The same problem did still exist.

I was not sure if any other .dll files were missing . Are there any solutions based on your experiences?

Q2. atlas

I wanted to use the atlas to define some WM tracts instead of manually drawing ROIs. HCP1065 tractography atlas (April 2020) provides subcomponents for cingulum, SLF, corticopontine track, corticostriatal track, corticothalamic track. In DSI Studio, in Step T3a, the drop-down list of atlas displays 80 different regions from HCP842 atlas without those new subcomponents mentioned above. However in Step B4(automatic fiber tracking) those new subcomponents are available for selection for fiber tracking.

Is there any way to add and display those new subcomponents for region assignments in Step T3a ?

Q3. automatic fiber tracking (Step B4)

In Step B4(a), if I input FIB files(from DTI reconstruction), the fiber tracking will automatically run but there is not any chance to setup some tracking parameters, which can be changed in Step T3c(options for tracking for individual FIB file).

Is there any way to setup the tracking parameters in Step B4 when input is FIB file?

Q4. FIB reconstruction

I uploaded one set of my SRC file and FIB file(from DTI reconstruction on a healthy subject). (20 directions, b-values=0 and 1000, thickness=3mm, in-plane resolution is 1.28mm, number of acquisition=2). Please take a look at the data files. Based on the imaging parameters and SNR of this scan, does it mean that DTI method is the most suitable method for FIB reconstruction ?

I am looking forward to hearing from you.

Thank you very much.

Best regards,

F.B.

Frank Yeh

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Feb 16, 2021, 4:05:10 PM2/16/21

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Q1. FIB files could not be loaded

I downloaded the latest version--Feb.3,2021 build.

I installed DSI Studio on my 64-bit laptop with Windows 7 + Microsoft Visual C++ 2012 Redistributable(X64). I could create the SRC file and FIB file , and do fiber tracking on the FIB file.

However, after I installed DSI Studio(same version) on my 64-bit desktop PC with Windows 7, DSI Studio could not start to run due to missing msvcp140.dll and vcruntime140.dll. I copied both of the .dll files from my laptop and installed them on my desktop PC. DSI Studio started then. But I could not load any FIB files to do fiber tracking(Step T3) because the window of fiber tracking could not be displayed. DSI Studio was not responding, without any error messages. I then installed Microsoft Visual C++ 2013 Redistributable(X64) (from the link on DSI Studio download page) . The same problem did still exist.

I was not sure if any other .dll files were missing . Are there any solutions based on your experiences?

Sorry I have no idea. You may try it on Windows 10 and see if it works.

Q2. atlas

I wanted to use the atlas to define some WM tracts instead of manually drawing ROIs. HCP1065 tractography atlas (April 2020) provides subcomponents for cingulum, SLF, corticopontine track, corticostriatal track, corticothalamic track. In DSI Studio, in Step T3a, the drop-down list of atlas displays 80 different regions from HCP842 atlas without those new subcomponents mentioned above. However in Step B4(automatic fiber tracking) those new subcomponents are available for selection for fiber tracking.

Is there any way to add and display those new subcomponents for region assignments in Step T3a ?

I will update the atlas to make them available, hopefully in one or two months.

Q3. automatic fiber tracking (Step B4)

In Step B4(a), if I input FIB files(from DTI reconstruction), the fiber tracking will automatically run but there is not any chance to setup some tracking parameters, which can be changed in Step T3c(options for tracking for individual FIB file).

Is there any way to setup the tracking parameters in Step B4 when input is FIB file?

Sorry, the parameters are fixed in Step B4.

Q4. FIB reconstruction

I uploaded one set of my SRC file and FIB file(from DTI reconstruction on a healthy subject). (20 directions, b-values=0 and 1000, thickness=3mm, in-plane resolution is 1.28mm, number of acquisition=2). Please take a look at the data files. Based on the imaging parameters and SNR of this scan, does it mean that DTI method is the most suitable method for FIB reconstruction ?

Yes.

Best regards,

Frank

I am looking forward to hearing from you.

Thank you very much.

Best regards,

F.B.

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F.B.

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Feb 16, 2021, 5:46:18 PM2/16/21

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Hi Frank,

Thank you for your quick responses and answers.

Regarding Q1: The download page of DSI Studio offers a link to "Update for Visual C++ 2013 and Visual C++ Redistributable Package". Does it mean that MS visual C++ 2013 is required for DSI Studio ?

Automatic Fiber Tracking(Step B4) could work on the FIB files which could not be opened in Fiber Tracking(Step T3) on my desktop PC. It seemed the GUI window for Fiber Tracking could not be displayed while the FIB file could be read for Automatic Fiber Tracking.

In Step T3, when FIB file was loaded, what DLL files were called so as to display the GUI window for fiber tracking ?

Hopefully these information may help you to figure out some solutions or ideas to Q1.

Thanks again.

Regards,

F.B.

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Frank Yeh

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Feb 16, 2021, 7:02:47 PM2/16/21

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It is likely that your graphic card drivers were not correctly installed.

Frank

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fenba...@gmail.com

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Feb 16, 2021, 7:25:56 PM2/16/21

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Thank you Frank. I will check them out.

F.B.

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F.B.

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Feb 17, 2021, 5:32:44 PM2/17/21

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HI Frank,

Per your suggestion, I checked the graphic cards on both of my laptop(Intel HD Graphics 4000) and desktop PC(NVIDIA NVS 510). Both drivers work properly. The driver for desktop PC was upgraded to the latest version (11/18/2019).

Actually I encountered the problem (i.e. FIB files could not be opened in Step T3) when I remotely run DSI Studio on the desktop PC from my laptop via Windows Remote Desktop Connection.

It seems the remote desktop connection blocked or disabled some features related to display or rendering.

.

Today I tried to run DSI Studio on the desktop PC locally. Step T3 worked !

I read an article which may explained something (GPU rendering for Microsoft remote desktop).

https://knowledge.civilgeo.com/knowledge-base/enabling-gpu-rendering-for-microsoft-remote-desktop/

I changed some settings on desktop PC and laptop by following the instructions in the following article.

https://blog.tedd.no/2011/04/28/optimizing-rdp-for-casual-use-windows-7-sp1-remotefx/

However the same problem still did exist during Microsoft remote desktop session.

Does DSI Studio have any specific requirements on the graphic cards for 3D display of images or fibers ?

Do you have any other insights to figure out the problem solving ?

Thank you very much.

Regards,

F.B.

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Frank Yeh

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Feb 17, 2021, 6:02:46 PM2/17/21

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Sorry I also have no idea. I used google remote desktop and it works okay.

Perhaps you may try other remote programs.

Best regards,

Frank

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