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Oct 21, 2016 07:10 PM | Yuta Aoki - The University of Tokyo
assurance of uniform distribution
Dear DTIPrep experts,
Could someone teach me how to quantify the uniformity of the distribution of directions?
We have DTI data with 64directions, and it looks like DTIPrep with default setting exclude 10 directions.
Before analyzing these data, I want to make sure the uniformity of distribution.
I would like to replicate the figure7 in the paper "DTIPrep: quality control of diffusion-weighted images" published in 2014.
I am using DTIPrep1.2.7.
Best,
Yuta
Could someone teach me how to quantify the uniformity of the distribution of directions?
We have DTI data with 64directions, and it looks like DTIPrep with default setting exclude 10 directions.
Before analyzing these data, I want to make sure the uniformity of distribution.
I would like to replicate the figure7 in the paper "DTIPrep: quality control of diffusion-weighted images" published in 2014.
I am using DTIPrep1.2.7.
Best,
Yuta
Oct 24, 2016 05:10 PM | Martin Styner
RE: assurance of uniform distribution
Hi Yuta
Well, the error estimates shown in rows 2 and 3 in that figure cannot be reproduced by DTIPrep (It is not difficult to do so, we just don't have the manpower to add this, as there is limited interest for that particular option).
With respect to the top row of that figure, that simply displays the surviving motion corrected gradients, that should be possible in DTIPrep. For that
- load the QCed DWI data as a new dataset into DTIPrep
- you may need to go to protocol and generate a default protocol, or you could load the protocol used to generated the QCed DWI
- go to the 3D display and you should be all set, i.e. you should see the sphere with directions etc
- set opacity to 1.0 (you may need to move it around to have an effect, there's a bug on that slider) to only see the ends of the gradient vectors
Well, the error estimates shown in rows 2 and 3 in that figure cannot be reproduced by DTIPrep (It is not difficult to do so, we just don't have the manpower to add this, as there is limited interest for that particular option).
With respect to the top row of that figure, that simply displays the surviving motion corrected gradients, that should be possible in DTIPrep. For that
- load the QCed DWI data as a new dataset into DTIPrep
- you may need to go to protocol and generate a default protocol, or you could load the protocol used to generated the QCed DWI
- go to the 3D display and you should be all set, i.e. you should see the sphere with directions etc
- set opacity to 1.0 (you may need to move it around to have an effect, there's a bug on that slider) to only see the ends of the gradient vectors
Oct 27, 2016 04:10 PM | Yuta Aoki - The University of Tokyo
RE: assurance of uniform distribution
Hi Martin,
Thank you for your swift response.
As far as I tried, DTIPrep1.2.7 does not display the top row of that figure, while DTIPrep1.2.4 did.
If it is not difficult, it would be greatly appreciated if you teach me how to reproduce the rows 2-3 figures so that I can try to reproduce them in my computer.
(since my background is clinical, it should not be easy for me...)
Best,
Yuta
Thank you for your swift response.
As far as I tried, DTIPrep1.2.7 does not display the top row of that figure, while DTIPrep1.2.4 did.
If it is not difficult, it would be greatly appreciated if you teach me how to reproduce the rows 2-3 figures so that I can try to reproduce them in my computer.
(since my background is clinical, it should not be easy for me...)
Best,
Yuta
Nov 2, 2016 01:11 PM | Martin Styner
RE: assurance of uniform distribution
Hi Yuta
Unfortunately the support to create image like those is not available in DTIPrep right now (and I don't know any tool that would be supporting this in a straightforward manner). We computed these with matlab and visualized with 3D Slicer (ParaView or ShapePopulationViewer would work great too). The computation of these take about 1 day per experiment (as these are simulation based error estimations).
Martin
Unfortunately the support to create image like those is not available in DTIPrep right now (and I don't know any tool that would be supporting this in a straightforward manner). We computed these with matlab and visualized with 3D Slicer (ParaView or ShapePopulationViewer would work great too). The computation of these take about 1 day per experiment (as these are simulation based error estimations).
Martin
Nov 10, 2016 04:11 PM | Yuta Aoki - The University of Tokyo
RE: assurance of uniform distribution
Hi Martin,
Thank you for your response.
I will try to make the image.
best,
Yuta
Thank you for your response.
I will try to make the image.
best,
Yuta