Setting different seed point or ROI

[maede...@gmail.com]

Dear Frank

I hope you are doing well.

in dsi studio when i set two regions as roi for example like: 

--action=trk --source="$f"  --fiber_count=20000  --thread_count=12 --turning_angle=30 --step_size=0.0 --min_length=2 --max_length=40  --fa_threshold=0.00 --otsu_threshold=0.7  --tip_iteration=2  --roi=DukeCIVM:HPF__Hippocampal_Formation_Uncharted_left --roi2=DukeCIVM:HPF__Hippocampal_Formation_Uncharted_right --export=stat,tdi  --output="$f".Both.trk.gz  > "${f}.log.txt"

it gives the tract passing between the ROIs, however I wanna extract all the tracts passing through either roi or roi2.Do u have any idea how I can do this? 

 and by the way can I replace "roi" by "seed" in this command? because when i do this it seems dsi ignores seed2 and it just takes the first region as seed point...

I would be grateful if u help me with this part as well

best

Maedeh 

[Frank Yeh]

> it gives the tract passing between the ROIs, however I wanna extract all the tracts passing through either roi or roi2.Do u have any idea how I can do this?

Merge them into just one roi instead of two.
Frank

[maede...@gmail.com]

Thank you very much dear frank, yes I could do it using DSI studio GUI, but for command line for example:  --action=trk --source="$f"  --fiber_count=20000  --thread_count=12 --turning_angle=30 --step_size=0.0 --min_length=2 --max_length=40  --fa_threshold=0.00 --otsu_threshold=0.7  --tip_iteration=2  --roi=DukeCIVM:HPF__Hippocampal_Formation_Uncharted_left --roi2=DukeCIVM:HPF__Hippocampal_Formation_Uncharted_right --export=stat,tdi  --output="$f".Both.trk.gz  > "${f}.log.txt"

how can I merge these two ROIs? I dont see in the documents of DSI studio.

Best regards

Maedeh

[Frank Yeh]

try

--roi=DukeCIVM:HPF__Hippocampal_Formation_Uncharted_left+DukeCIVM:HPF__Hippocampal_Formation_Uncharted_right 

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[maedeh khalilian]

It worked . Thank you so much.