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)?

Preclinical Imaging

Submitted by davb63 on Fri, 07/05/2019 - 09:45

Dear Tortoise Community.

I just found the different tools offered by Tortoise and I was impressed !

I am a preclinical imaging scientist and I am in trouble to deal with diffeomorphic normalization of my DTI data.

I would like to know if Tortoise could adress preclinical data like rats and sheep (I developped atlases, templates (T2) and GM, WM and CSF priors associated to my dwi images).

The last step is to create a DTI template of each so do you think that I am at the good place ?