DIFFPREP

Hi,

I am trying to run DIFFPREP and I am getting the following error message:

Denoising DWIs...

Segmentation Fault: 11

The data that I am using is 220 total volumes with 3 shells (1000, 2000, 3000). I know this error is sometimes caused by memory issues but I have 32GB of RAM, which should be plenty I think. Does anyone know what may be causing the issue? 

Thanks,

Brady

Hello Tortoise Support!

What is the most straightforward way to get an estimate of my subject's head motion from the pre-processing pipeline?  Can the parameters from the rigid-body registration of each volume be extracted from one of the output files?

Thanks, Joelle

Dear Tortoise Team,

Thanks for your wonderful support and your new fast and awesome Tortoise 3.1.4!

Hi all,

I am trying to use TORTOISE to susceptibility-induced distortion correction on my DTI and I've selected the option ANTSSyN, However, in the log files, I am not seeing a nonlinear registration file, or even an affine registration file. I also don't see a reference to a nonlinear registration in the console window. Moreover, I see some areas where the deformation is not quite working. Am I missing something?

Hi

I was trying to run the rodent data on the tortoise, i was not sure about what is big bang in the diffprep module. What are the correct default settings for rodent data, all I have is, a 2 b-values, 14 directions, spin-echo based DTI data? Anything I have to uncheck before running this?

what is big delta and small delta in the import module? is this time between two diffusion gradients and separation? or something else?

I have a good AC-PC aligned T2star image for each subject that aligns well with the DTI for most subjects, but some DTI alignment with this T2star ACPC image is poor.  Are there alignment options within the DIFFPREP command to improve this?

Thanks!

Becca

Dear TORTOISE group,

Thank you for an updated software version. I have used TORTOISE long time ago when it had only the GUI version.

Using .nii file as my DWI Nifti file, keeps saying does not exist, I have tried putting full path to file all the way from root and still not being found. 

Greetings!

I get this error message right at the start of every run:

** Cannot find '@chauffeur_afni' from AFNI:
.: Event not found.
** Cannot find '@djunct_4d_imager' from AFNI:
.: Event not found.
Denoising DWIs for use in registration..

And this message at the very end of every run: