General discussion

Calling TORTOISE modules from Python

Submitted by tecork on Sun, 10/03/2021 - 20:01


I have had TORTOISE for a while now and was interested in incorporating the modules into my workflow. I am on MacOS Catalina (Version 10.15.7). and using python 3. I can run the following command from the terminal just fine:

ImportNIFTI -i /Users/Tyler/Vol_1_LR.nii -b /Users/Tyler/Vol_1_LR.bval -v /Users/Tyler/Vol_1_LR.bvec -p vertical

However, when I run it using subprocess in Python 3, like the following:

>>> import subprocess


Submitted by Ashika on Thu, 12/24/2020 - 03:54

Hi Experts,

We have tried to install Tortoise on Redhat 7 using the installation instructions given for LINUX (https://tortoise.nibib.nih.gov/tortoise/v313/1-installing-tortoise)

While executing the last command "bash install_TORTOISE.bash" it failed to install tortoise and throws up an error as attached in tortoise.pdf .

Kindly suggest the needful


Import* and Compute* commands exit codes not zero

Submitted by szhang on Tue, 07/28/2020 - 11:43

Hi experts,

I noticed that the Import* from diffprep & Compute* from diffcalcv3 had non-zero exit codes (e.g. echo $?) when they completed. They ran fine locally, but when running in docker images (from latest ubuntu:18.04), they would exit the image because of this. Is there any consideration of letting the exit code be non-zero? Any insight would be appreciated.



Running TORTOISE through Matlab

Submitted by m.spriggs on Fri, 04/24/2020 - 12:09


I am new to TORTOISE and would like to use it within scripts written in Matlab. I have installed the toolbox to successfully use through the terminal, however, when I run it through Matlab using the command 


I get the following error:

dyld: Library not loaded: /usr/local/opt/llvm/lib/libomp.dylib
  Referenced from: ... /TORTOISE_V3.2.0/DIFFPREPV320/bin/bin/DIFFPREP
  Reason: image not found

I am unclear on how to address this so any assistance would be very welcome. 


Brain Parcellation Map Output?

Submitted by smeisler on Sat, 04/11/2020 - 16:54


I would like to use the output of TORTOISE into a FreeSurfer tool called AnatomiCuts to cluster white matter streamlines. The main inputs are a streamline file in .vtk format, and a .nii segmentation file. I have two questions regarded to the creation of these files.

1) I know from the GUI export menu that .vtk is natively supported by TORTOISE. However, I would like to keep the whole process in the command line. Is there a way to script this kind of export?

2) Does TORTOISE at any point output a brain map segmentation file (xxx_parc.nii.gz for example)?