Dear users and developers,
I am using DTIPrep 1.2.4 in a pipeline (no GUI) and apparently works fine, but I have some doubts on reading the QC report. Are there some instructions or a tutorial on how to read it? In particular I am interested on gradient remove info: in a subject i get gradient 22 removed because:
======
Slice-wise Check Artifacts:
Region Gradient# Slice# Correlation
whole         22 8    0.816240
=====================

but looking at gradient DWI I didn't see any hugly and slice 8 to what refer? native slice 8 in z axis? It is too low.
Eventually can I send you the dataset or the dwi volume 22?
Thanks in advance,
cheers,
Giuseppe

Hi Giuseppe
In the docs section on NITRC you find a manual that should provide some information.

Wrt your QC report txt file: Yes, this would be gradient index 22 (starting at index 0, so it's the 23rd DWI volume). Slice 8 is the native  slide 8 (again starting at index 0, so it's the 9th slice).

If that slice is actuallyfine, but at the full bottom or top of the brain then you need to increase the head skip (resp tail skip) parameter, so that it does not check there. The slices at the bottom and at the full top of the brain need to be skipped, as the slice wise check is based on consistency across slices and if the slice content, i.e. anatomy, changes dramatically from one slice to the other, then DTIPrep will flag that slice, even though the inconsistency is not due to an artifact.

Martin

Originally posted by Giuseppe Cabras:

Hi everyone,
we are trying to implement DTIPrep in our study. Unfortunately we are unsure of how to interpret the output of the Diffusion Gradient Check. 5-10% of subjects are excluded due to a mismatch in diffusion gradients in some dw-directions. What does that mean? When visually inspecting the images, we found no changes or artifacts. How should we proceed? Exclude these participants from analysis alltogether, exclude the affected directions or ignore the error in absense of observable artifacts?

Thanks in advance!
Susanne

 
Originally posted by Susanne Meinert: Hi Susanne

The Diffusion Gradient Check is not well named (we should probably change that), as it detects residual motion that the prior motion & eddy current correction step was not able to correct.

The default settings of that Diffusion Gradient Check step are quite aggressive (another thing to definitely change), and thus it could be that DTIPrep is removing acceptable images. One way to diagnose whether that is the case is to turn this step off and look at the otherwise-rejected DWIs and see whether they show motion compared to the other DWIs. If so, you should increase the thresholds. Alternatively, you could also just increase the thresholds and look at the output and see whether you see increased residual motion in the output DWI. If not, then you are fine with the increased thresholds.

In our own studies, we commonly use larger thresholds than the defaults. We use 1.5 - 2 x voxelsize for the translation and 1 - 1.5 degrees for rotation.

Martin