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General discussion

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.

Best,

Shengwei

Running TORTOISE through Matlab

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

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!

Brain Parcellation Map Output?

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

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)?

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 ?

 

David

Running ComputeGlyphMaps under Linux: error message 'Aborted'

Submitted by timschaefer on Fri, 03/01/2019 - 09:15

Since I was unable to get ComputeGlyphMaps to work under MacOS, I tried under Linux. I installed v3.1.3 for Linux on an Ubuntu 16.04 LTS server and once more followed the manual up to the part where ComputeGlyphMaps is run. Then I run ComputeGlyphMaps:

$ ComputeGlyphMaps subject1dti_proc/subject1dti_L0_DT.nii
subject1dti_proc/subject1dti_L0_DT_2_36.png
Aborted

Running Tortoise 3.1.2 under recent MacOS versions (High Sierra, Mojave)?

Submitted by timschaefer on Fri, 03/01/2019 - 08:31

We installed Tortoise 3.1.2 from here under MacOS (we tried both High Sierra and Majave, the latest 2 versions) and followed the manual to process our data. But at the first step (data import), the ComputeGlyphMaps command fails:

When running ComputeGlyphMaps, I get the following error (even when running witout any command line arguments):