Hello ,
My name is MC kim, and I need some help.
The DTIPrep version I got is 1.2.4.
I try to preprocess my DWI images with DTIPrep, and I got some questions in doing it. 

1) I initially tried with 'default' protocol, and DTIPrep excluded 17 out for 31 gradients from a DWI data set from a subject.
the reason was due to interlace artifact. When I visual checked the DWI data, I couldn't agree that much artifact. 
I attached the captured QC result file.

I tried preprocessing again, and this time I changed the protocol, instead of using 'default'.
By default, DENOISING_bCheck, JOINDENOISING_bCheck, BRAINMAST_bCheck, and DOMINANTDIRECTION_bCheck at setted "No", and I changed settings into "YES"
As I tried again with all "YES" all of the directions were included in QCed DWI.
Thus I though by changing protocols to all "YES", the protocol became more tolerant to artifact.

My question is is it okay to run with the protocol setting of all "YES"? Is there any potential problem?

2) Even though the "default"protocol excluded more than half of DWI gradient directions, DTIPrep still generated DTI images such as FA, MD, etc.
Can I use this DTI image to analysis or tract generation? or should I prepration again with different protocol setting.

3)I read that DTIPrep has two nice functions, those are "vibration artifact checking" and "simulation based bias analysis".
I want to know which parameter on protocol setting represents those functions.
My guess is "DOMINANTDIRECTION_bCheck" maybe vibration artifact correction, am I right?

4) When I click on "Default" protocol, I get the error message saying "The following programs have not been found. Please enter the path manually if necessary> DiffusionWeightedVolumeMasking"
Can you tell me where can I get this program or how can I solve the problem?

Thanks in advance and I look forward to hear from you.

MC Kim