DSI Studio crash computing connectivity matrix - GUI and commandline

[James Hengenius]

Hi Frank,

I ran into this problem running the February 26, 2021 version of DSI Studio.

I have a whole brain trk file and a binary lesion map included in my fib file. I want to compute the lesion burden between ROIs using the following command in the GUI [Tracts][Connectivity matrix...]:

Parcellation atlas: ROIs, end region. Value: lesion, threshold by 0.00100 of the sum

When I click Recalculate, DSI Studio crashes. I attempted the same in the commandline:

dsi_studio --action=ana --source=HCP201_dsistudio.fib.gz

         --tract=HCP201_dsistudio.trk.gz 

         --connectivity=native_MMP.nii.gz 

         --connectivity_value=qa,count,ncount,lesion 

         --connectivity_type=pass,end

The program progresses until it tries to compute the lesion matrix, then it quits It does not produce and error message:

DSI Studio Feb 26 2021, Fang-Cheng Yeh 

source=HCP201_dsistudio.fib.gz 

action=ana 

loading HCP201_dsistudio.fib.gz... 

tract=HCP201_dsistudio.trk.gz 

loading HCP201_dsistudio.trk.gz... 

loading HCP201_dsistudio.trk.gz 

HCP201_dsistudio.trk.gz loaded 

connectivity=native_MMP.nii.gz 

connectivity_type=pass,end 

connectivity_value=qa,count,ncount,lesion 

loading native_MMP.nii.gz 

DWI dimension=(157,189,136) 

NIFTI dimension=(260,311,260) 

nifti loaded as multiple ROI file 

looking for region label file 

no label file found. Use default ROI numbering. 

NIFTI file has a different dimension from DWI. 

applying QSDR warpping to the native space NIFTI file 

a total of 360 regions are loaded. 

connectivity_threshold=0.001 

count tracks by passing 

calculate matrix using qa 

export connectivity matrix to HCP201_dsistudio.fib.gz.native_MMP.qa.pass.connectivity.mat 

export connectogram to HCP201_dsistudio.fib.gz.native_MMP.qa.pass.connectogram.txt 

export network measures to HCP201_dsistudio.fib.gz.native_MMP.qa.pass.network_measures.txt 

connectivity_threshold=0.001 

count tracks by passing 

calculate matrix using count 

export connectivity matrix to HCP201_dsistudio.fib.gz.native_MMP.count.pass.connectivity.mat 

export connectogram to HCP201_dsistudio.fib.gz.native_MMP.count.pass.connectogram.txt 

export network measures to HCP201_dsistudio.fib.gz.native_MMP.count.pass.network_measures.txt 

connectivity_threshold=0.001 

count tracks by passing 

calculate matrix using ncount 

export connectivity matrix to HCP201_dsistudio.fib.gz.native_MMP.ncount.pass.connectivity.mat 

export connectogram to HCP201_dsistudio.fib.gz.native_MMP.ncount.pass.connectogram.txt 

export network measures to HCP201_dsistudio.fib.gz.native_MMP.ncount.pass.network_measures.txt 

connectivity_threshold=0.001 

count tracks by passing 

calculate matrix using lesion 

export connectivity matrix to HCP201_dsistudio.fib.gz.native_MMP.lesion.pass.connectivity.mat 

export connectogram to HCP201_dsistudio.fib.gz.native_MMP.lesion.pass.connectogram.txt 

export network measures to HCP201_dsistudio.fib.gz.native_MMP.lesion.pass.network_measures.txt 

Any help would be greatly appreciated!

[Frank Yeh]

Could you upload the files in a zip file?
I will check the problem and get back to you.
Frank

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[James Hengenius]

Sure Frank - I just uploaded the fib, trk, and ROI files. 

Jim

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[Frank Yeh]

I updated DSI Studio to fix this bug.

Please test if it works for you.

Best,

Frank

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[James Hengenius]

Thanks Frank!

I just tested it out and the connectivity matrix now works when computed from the GUI and the command line.

Jim

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[James Hengenius]

Hi Frank,

Thanks for fixing this so quickly. Follow-up question: Is this fix reflected in the current Mac version of DSI Studio as well? One of my collaborators is on Mac and would like to run this analysis on his computer. (I'm on a Windows PC so I can't test the Mac version myself.)

Thanks!

Jim

[Frank Yeh]

Yes, it is updated (today's version).

Frank

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