Question Regarding QC

[Cristina Roman]

Hello, 

I have recently begun using TORTOISE for motion and eddy current correction prior to TBSS. I ran my 4D FSL NIFTI files through DIFF_PREP, using the default settings. Prior to converting my data back into FSL format (using DIFF_CALC's "export images"), I imported my DIFF_PREP data (...DMC.listfile) using "load listfile" and then viewed my data using "display raw images." Some of the images are cut off, however, and I wanted to know if this might just be a function of the "display" application, or might there be something wrong with my data? I have attached some snapshots for your reference. 

In addition, might you be able to confirm where I would jump in for the TBSS analyses after running my data through DIFF_PREP? Currently, my pipeline involves the following: averaging B0's and replacing the 1st B0 with the average, eddy current correction, brain extraction (bet), dtifit, and then the actual TBSS analysis. Would it now be: TORTOISE DIFF_PREP, averaging B0's and replacing 1st B0 with average, brain extraction, dtifit, and then TBSS? 

Thank you in advance for your kind attention and help as I learn how to navigate TORTOISE. 

Sincerely, 

Cristina