command line for saving tract density end points

[jli...@gmail.com]

Hello,

We're trying to command line option for exporting the endpoint tract density image.

We ran this command successfully and got the tracking output and the tract density output.  We also ran --export=tdi2 and got the result in subvoxel space.

'! C:\Users\jlin\Downloads\dsi_studio_64\dsi_studio --action=trk --source=' storet1control{x} ' --seed=HarvardOxfordSub:Right_Amygdala '...

        '--seed_count=1000000 --step_size=0.25 --turning_angle=60 --fa_threshold=0.1 --smoothing=0.85 --min_length=20 '...

        '--max_length=300 --output=D:\Analysis\DSI\tract_density\storet1control\' storet1control{x}(1:10) '_R_Amgydala.trk '...

        '--export=tdi'

We looked in the documentation but could not find the flag for this option.

Thanks!
Jo

[Fang-Cheng Yeh]

Hi Jo,

    Can you provide more detail about what you would like to get from the command line here? (TDI or TDI2?). You may also send me the log output to debug.

Best regards,

Frank 

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[Joanne Lin]

Hi Frank,

Sorry for the delay in replying to you.

The output we were hoping to get from the command line was the tract density endpoint map.  Inside the gui, after tractography, we right click on the result > save tract density > diffusion space > "No" (to save in NIfTI format) > "No" (to save endpoints, rather than whole tracts)

TDI and TDI2 didn't quite give the output we were after so we were wondering whether there was an option/flag to do this in the command line.  

Thanks!
Jo

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[Fang-Cheng Yeh]

Hi Jo,

Could you send me the log output of the commandline? DSI Studio
won't export TDI if there is a problem in the preprocessing.

Best regards,
Frank

[Joanne Lin]

Hi Frank,

Here is the log output from the analysis -

DSI Studio Jan  5 2015, Fang-Cheng Yeh 

loading 01_T1.dti_data.nii.gz.src.gz.odf8.f5rec.bal.fz.reg0.qsdr.1.25.2mm.R60.fib.gz... 

seed_count=1000000 

Loading Right_Amygdala from HarvardOxfordSub atlas 

loading atlas... 

HarvardOxfordSub loaded. 

loading template C:/Users/jlin/Downloads/dsi_studio_64/HCP488_QA.nii.gz 

Transformation matrix found. 

seed=HarvardOxfordSub:Right_Amygdala 

turning_angle=60 

fa_threshold=0.1 

step_size=0.25 

smoothing=0.85 

min_length=20 

max_length=300 

tracking_method=0 

initial direction=0 

interpolation=0 

voxelwise=0 

thread_count=1 

start tracking. 

finished tracking. 

a total of 639766 tracts are generated 

output file:D:\Analysis\DSI\tract_density\storet1control\01_T1.dti__R_Amgydala.trk 

saving 

export TDI to D:\Analysis\DSI\tract_density\storet1control\01_T1.dti__R_Amgydala.trk.tdi.nii.gz 

calculating 

Thanks!

Jo

[Fang-Cheng Yeh]

Hi Jo,

I will open the option for exporting the endpoint TDI in the
command line. Once it is available in the new release, I will notify
you.

Best regards,
Frank

[Fang-Cheng Yeh]

Hi Jo,

I updated DSI Studio. Now you may use export=tdi_end to get the
endpoint TDI. The mac version will be updated after March 1.

Best,
Frank