General discussion

Hello, 

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

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

Dear Tortoise team,

I have some questions about the changes of histogram of b0 image after preprocessing including motion & eddy distortion correction, EPI correction (using DRBUDDI), gibbs ringing correction, denoising.

Hi, I wondered if you have any plans to run a training course (virtual/face-to-face/hybrid) this year or in 2021, please? I'm try to plan training for students and it would be great to know, if so. Many thanks, Ryckie Wade

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.

Best,

Shengwei

Hi,

Just wonder what the unit should be for the ImportNIFTI -d & -D options (is it ms or sec.)? Also, how are these options used in the downstream analyses?

Thanks,

Shengwei

Hello, 

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 

!DIFFPREP

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
DIFFPREP: Aborted

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

Thanks!

Hello,

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)?

Dear community,

where can I find the source code for TORTOISE? Thank you for your help :-)

Lea

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 ?

David