open-discussion
open-discussion > RE: Visual check of the DTI data
Mar 29, 2020 10:03 PM | ameliaqian
RE: Visual check of the DTI data
1. In the DTIPrep manual, denoising is not default. One
collaborator recommended me to denoise the DTI data. I wonder in
which circumstance I should implement denoise procedure and how it
influences the final analysis?
2. One participant are failed from DTIPrep pipeline with the reason "Single b value DWI without a b0/baseline". But when I checked this participant, it does have b0 and 64 gradients. What does this failing reason mean?
3. You mentioned "slice wise check detected an artifacts (mainly based on a low correlation of this slice to its neighboring slice)". I want to know whether DTIPrep calculates the correlation of this slice to its previous neighboring slice or more?
4. I found I cannot implement visual check 2: "Directional Spatial Distribution QC". I can only see the lines starting from the centre of sphere, rather than dots. The lines change color when I move the sphere. So I cannot identify the location of excluded gradients. My version of DTIPrep is 1.2.4.
5. I notices b0 in one brain scan have artifacts in raw data but corrected in QCed.nrrd. Should I excluded this participant in this case?
6. I am trying to test the effect of NC on the DTIPrep output. Is it the parameter "SLICE_correlationDeviationThresholdGradient"? Also, I wonder if I change this parameter from 3.5 to 1, whether I need to change the parameter "SLICE_correlationDeviationThresholdbaseline" correspondingly?
2. One participant are failed from DTIPrep pipeline with the reason "Single b value DWI without a b0/baseline". But when I checked this participant, it does have b0 and 64 gradients. What does this failing reason mean?
3. You mentioned "slice wise check detected an artifacts (mainly based on a low correlation of this slice to its neighboring slice)". I want to know whether DTIPrep calculates the correlation of this slice to its previous neighboring slice or more?
4. I found I cannot implement visual check 2: "Directional Spatial Distribution QC". I can only see the lines starting from the centre of sphere, rather than dots. The lines change color when I move the sphere. So I cannot identify the location of excluded gradients. My version of DTIPrep is 1.2.4.
5. I notices b0 in one brain scan have artifacts in raw data but corrected in QCed.nrrd. Should I excluded this participant in this case?
6. I am trying to test the effect of NC on the DTIPrep output. Is it the parameter "SLICE_correlationDeviationThresholdGradient"? Also, I wonder if I change this parameter from 3.5 to 1, whether I need to change the parameter "SLICE_correlationDeviationThresholdbaseline" correspondingly?
Threaded View
Title | Author | Date |
---|---|---|
ameliaqian | Feb 28, 2020 | |
Martin Styner | Mar 23, 2020 | |
ameliaqian | Mar 23, 2020 | |
Martin Styner | Mar 23, 2020 | |
ameliaqian | Mar 24, 2020 | |
ameliaqian | Mar 23, 2020 | |
Martin Styner | Mar 23, 2020 | |
ameliaqian | Mar 29, 2020 | |