From GUI to Commandline Connectivity Matrix calculations

[Timothy Jordan]

Hi,

I'm sorry if this has been asked, but I couldn't find exactly what I was looking for in previous posts.

I am trying to make the command line script for Fiber Tracking between 2 ROI and then calculating the Connectivity Matrix for nqa,qa,and counts. I have done this in the GUI and have results from that, but when I try to do it in command line, everything comes out as 0.

This are the commands I have tried to no avail. If you can, please let me know what I am doing incorrectly. The 2 ROI are saved from the Freesurfer Atlas to make them easier to find for me.

1. dsi_studio --action=ana --source=eddy_corrected_data.nii.gz.src.gz.hcp1065.qsdr.1.25.R81.fib.gz --tract=track.tt.gz --connectivity=left_insula.nii.gz,posterior_cingulate.nii.gz --connectivity_threshold=0.1 --connectivity_value=qa,nqa,count --connectivity_type=pass,end > "test.txt"

2. dsi_studio --action=trk --source=eddy_corrected_data.nii.gz.src.gz.hcp1065.qsdr.1.25.R81.fib.gz --roi=left_insula.nii.gz --roi2=posterior_cingulate.nii.gz --seed_count=50000000 --fa_threshold=0.1 --output=no_file --connectivity=left_insula.nii.gz,posterior_cingulate.nii.gz --connectivity_threshold=0.1 --connectivity_value=qa,nqa,count --connectivity_type=pass,end > "test.txt"

3. dsi_studio --action=ana --source=eddy_corrected_data.nii.gz.src.gz.hcp1065.qsdr.1.25.R81.fib.gz --region=left_insula.nii.gz,posterior_cingulate.nii.gz

Thank you,

Tim

[Frank Yeh]

Sorry for missing your thread (Gmails sends it to SPAM)...

Did you use the most updated version of DSI Studio?

Some of the command line may not work in older versions.

If updating DSI Studio does not work out, you may post the log output here (the "test.txt") file.

Hope this helps,

Frank