FAQ

1. I have some data imported and used with TORTOISEV3. Can I just use TORTOISEV4 with it now?

   NO. TORTOISEV3 and TORTOISEV4 are incompatible. How they interpret the NIFTI image header AND their Bmatrix coordinate system are different. TORTOISEV4 now uses "ijk" coordinate system for its diffusion gradients and typically the x-direction is flipped between the two. This obviously applies to both the Bmatrix and the computed diffusion tensors and MAPMRI.

2. There is no ImportDICOM in TORTOISEV4. How do I then convert my DICOMs into NIFTI?

   TORTOISEV4 is now compatible with the most standard conventions. The reason why it needed a separate ImportDICOM before was because TORTOISEV3 was not. Now, you can use dcm2niix_directly to import your data.

3. What is even different between V3 and V4? Can I just keep using V4?

   V4 is a completely new code and nearly all existing aspects have been improved except denoising and inter-volume motion and eddy currents distortion correction. If those two are the only things you want to process for, yes, you can keep using TORTOISEV3. However, if you want the improved version of existing tools, such as gibbs ringing correction or susceptibility distortion correction, OR if you want to take advantage of new features such as slice-to-volume registration, outlier detection replacement, signal drift correction, gradient nonlinearity processing, then you need to switch to V4.

4. Is V4 faster than V3?

   If you have a CUDA capab;e NVIDIA GPU and driver, then yes it is significantly faster.

5. What about DRTAMAS??

   Because of some implementation changes, DRTAMAS has only been recoded for CUDA and not the CPU. NAturally, it uses V4-computed tensors and is not compatible with the V3 ones.

6. How do I check if my gradients and NIFTI are compatible with TORTOISEV4?

   The old way of looking at the non-symmetric DEC map is not applicable anymore. There are now two executables for this purpose. ComputeGlyphMaps which is an interactive tool but requires source code compilation (not available in docker) or the ComputeLineField which is non-interactive, outputs PNGs but works everywhere.

7. Where can I get help?

   Both the Github page and AFNI forums are the right places for your questions.

8. How do I cite TORTOISEV4?

   For now you can cite te TORTOISEV3 version but a mansucript for V4 has been submitted and under review. This entry will be updated when it is published.

The following questions are for TORTOISEV3 only

1. Does TORTOISE run on all operating systems?

   -- TORTOISE currently runs on Linux and MAC. Unfortunately for the moment we have discontinued the support for windows. If you do use Windows 10, TORTOISE can be run using the "Windows 10 Ubuntu subsystem".

2. How different are the versions 3.0 and above of TORTOISE compared to 2.5.2 and below?

   -- Versions 3.0 and above TORTOISE modules can be run from command line. This enables batch processing and command scan be easily incorporated into scripts without the interference of IDL gui as with previous versions.

3. Have lot of features changed between the IDL version and the new command line version of the software?

   -- A few additional features have been introduced in the versions 3.0 and above, such as gibbs ringing correction, denoising,  ANTSsyN EPI correction in DIFFPREP, additional features in DRBUDDI etc.

4. Can you combine processing from two different versions of the software?

   -- We highly recommend not combining processing results from two different versions of the software.