Modified mec files

Submitted by ajevia on Thu, 07/16/2020 - 18:53


I have a few questions about the mec files for DIFF PREP.

I am using DIFF PREP on ex-vivo specimens that are not expected to move during the scan.
Is it possible to create a mec file that corrects only for eddy currents but not motion?

In the mec file, there are optimization and bracketing epsilons.
How are these epsilons used during the optimization process?

Using T1 structural data

Submitted by smeisler on Sat, 04/11/2020 - 16:25


I would like to use TORTOISE on a data set for which T1, and not T2, structural data were collected. I read about a work-around for using T1 images here which seems to involve attenuating non-brain regions. Apparently this suggestion came from a TORTOISE developer. I just want to make sure that this would be valid and/or necessary to do in the most recent version of TORTOISE (3.2.0 at time of writing). 




Segmentation Fault: 11

Submitted by willi3by on Tue, 09/17/2019 - 13:12


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? 




Motion estimate

Submitted by sarllsjo@mail… on Tue, 08/27/2019 - 14:15

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


SyN registration

Submitted by hoptman on Mon, 07/22/2019 - 18:05

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?

re: rodent data

Submitted by nmskhan on Tue, 07/16/2019 - 17:08


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?