Can't see ROI's during Step3

[Benjamin Davidson]

Hi there and thanks in advance for any advice!

I'ved used DSIstudio to import DICOM files of a diffusion MRI to make an src, I then co-registered to a T1 structural from that same scan using [Edit] to [T1wspace]. It then successfuly made a fib and the tracts look great! However, I'm trying to upload an ROI I drew on the structural, and dsi-studio doesn't seem to reocgnize/see it. It shows up on the left as an ROI, but when I do 'fiber tracking' it ignores the ROI and does a WHOLEBRAIN (although if I hand-draw an ROI in dsi there's no issue). 

Any help would be greatly appreciated!

Ben

[Fang-Cheng Yeh]

Hi Ben,

Could you upload the fib, t1w, and the ROI for me to test the bug?

Thanks,
Frank

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[Benjamin Davidson]

Thanks Frank! Just uploaded. 

[Fang-Cheng Yeh]

Did you also get tractography like this? If yes, then you will find all tracks shown here are all passing the ROI.  This can be validated using use [Edit][Select] to single out track bundles.

There are a lot of false continuations, and you would need to adjust tracking parameters to reduce this error.

 

Selecr

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[Benjamin Davidson]

Hi Frank,

Thanks for your reply! You're right, yes I'm now able to see the ROIs, but my issue now I believe pertains to diffusions vs structural space and how to reconcile the two. I have postop t1 and DTI images, I traced two lesions on the T1 image, and want to use these as ROI's in the postop diffusion space. I tried to 'co-register' using dsi during step 2, by selecting 'edit' and 'to T1s space...' but my ROI's are still no lining up properly - they're supposed to be on the right and left anterior limb of internal capsule...

On Saturday, March 16, 2019 at 12:48:47 PM UTC-4, Benjamin Davidson wrote:

[Fang-Cheng Yeh]

Please update DSI Studio and see if it works for you?

Frank

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[Benjamin Davidson]

Thanks Frank. How do I update dsi on ubuntu?

Ben

On Saturday, March 16, 2019 at 12:48:47 PM UTC-4, Benjamin Davidson wrote:

[Fang-Cheng Yeh]

You would need to compile it or use docker: http://dsi-studio.labsolver.org/dsi-studio-download

Best regards,

Frank

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[Benjamin Davidson]

Frank I apologize in advance, it's probably obvious I'm a computer noob. I promise I looked through forums etc for an answer before asking you...I'm trying to use Docker to get the latest DSI version (I had a really hard time compiling before and not sure how to get the latest version that way). I believe I have now installed docker properly, and following the instructions I could find, I'm running

docker run -ti --rm -e DISPLAY=$DISPLAY \
                    -v /tmp/.X11-unix:/tmp/.X11-unix \
                    -v $PWD:/data \
                    manishka/dsi-studio-docker:latest

But I'm getting this error:

No protocol specified
QXcbConnection: Could not connect to display :0
Aborted (core dumped)

and I can't figure out a way forward!

Thanks a million

On Saturday, March 16, 2019 at 12:48:47 PM UTC-4, Benjamin Davidson wrote:

[Fang-Cheng Yeh]

It seems to me that this is an X windows connection problem. Unfortunately, I am also not familiar with the Linux system and not able to give you much of a help here. 

Best,

Frank

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[Benjamin Davidson]

No problem Frank, I got it working!

I realize what part of my confusion is - when I upload dicoms etc into dsi studio, it seems to be automatically processing everything into MNI space - is there any way for me to keep everything in the patient's native space? Those ROI's are drawn in patient space, which explains why they aren't in the anterior limb of the capsule!

On Saturday, March 16, 2019 at 12:48:47 PM UTC-4, Benjamin Davidson wrote:

[Fang-Cheng Yeh]

If you use GQI reconstruction, then it will be in subject's native space.
Frank