automation for tracking to endpoint images?

[Andrew Gerlach]

Hi Frank,

I have a dataset of older adults with a high white matter hyperintensity burden and am interested in lesion mapping approaches for looking at what gray matter areas may be disrupted by these WMH (similar to this). I have binary masks of WMH regions for each participant derived from T2FLAIR images normalized to MNI space, and I'd like to
1) use them as ROIs for tract tracing using the HCP-1065 average fiber template
2) save the endpoints to a .nii file for group level analysis

I am able to do this by clicking through the GUI with the following steps:
Regions-> Open Region -> set Type to ROI

Step T3d -> Fiber Tracking

Regions -> Delete Region

Tracts -> Endpoint to Region

Regions -> Merge Checked Regions

Regions -> Save Current Region As...

I tried using Records -> Command History to save the commands, but when I try to repeat the commands without any modification, I get an error that says "unknown command: 0:0" during the tracking step. It doesn't appear that the region type ever gets set to ROI. Here's the contents of the command file:

open_fib,/Users/gerlachar/Downloads/HCP1065.1mm.fib.gz,,
set_zoom,0.500000,,
open_region,/Users/gerlachar/Downloads/w802775_wmh.nii,,
run_tracking,w802775_wmh,c9A99193Fb803FdbF041b4843db803FcCDCC4C3Ec 0:0,
delete_region,0,,
endpoint_to_region,0,,
merge_regions,0&1,,
save_region,/Users/gerlachar/Downloads/w802775_wmh endpoints1.nii,0, 

Do you have any suggestions on how I can automate this process for our ~100 subjects?

Thanks!
Andrew

[Frank Yeh]

Thank you for reporting this issue.

I will fix the bug and get back to you.

Frank

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[Frank Yeh]

You may update DSI Studio again to fix the bug, and follow the following steps:

1. Do the same as what you did, and save the endpoint in another folder.
2. After saving the file, delete all regions and all tracts.

3. In the command history, drag to select steps from the 'open_region' steps to the last one (which is delete_region or delete_tract).
4. Click on the 'Apply to Files' button, select all NIFTI files that you would like to repeat the steps.