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MRtrix3 / mrtrix3

MRtrix3 provides a set of tools to perform various advanced diffusion MRI analyses, including constrained spherical deconvolution (CSD), probabilistic tractography, track-density imaging, and apparent fibre density
http://www.mrtrix.org
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mrview screen capture #121

Closed phiweger closed 10 years ago

phiweger commented 10 years ago

Dear mrtrix experts,

I am struggeling with the screencapture in mrtrix3.

1. It used to be possible to capture a whole stack of screen shots in say the axial orientation. What do I have to do in mrtrix3 to replicate this? It seems trivial, but after trying to set for example translation z to 50, and choosing an index from 1 to 50, I nevertheless only get screenshots of the same image over and over.

2. I tried the batch mode also, but something like

mrview -batch batch.txt T1.nii.gz

where batch.txt contains

tractography.load tracks.tck

gives me this error:

mrview [WARNING]: batch command "capture.grab" unclaimed by main window or any active tool - ignored

if I write exit in the batch.txt file, it exits mrview as it is supposed to do.

Thank you very much for your help, Best, Adrian

jdtournier commented 10 years ago

Hi Adrian,

  1. yes, it's just a matter of setting the translation values and the number of frames you need. The viewer will then grab that number of screenshots equally spaced between your current location and the location given by your requested translation.
  2. you need to start the tractography tool before any tractography-related commands can be interpreted. So add the line 'tool.open 3' at the start of your script.

Can I also ask you to direct these types of queries to the MRtrix3 Google+ forum? The GitHub tracking system really is about tracking bugs and issues with the software itself rather than its use...

Cheers, Donald.

draffelt commented 10 years ago

Hi Adrian, Just one more point. Currently the translation occurs along the scanner coordinate axis. If your image axis and scanner axis are not aligned (which will be indicated by a rotation in the transformation output by mrinfo), then the image may 'shift' as it translates along the desired axis. We will include a 'image axis' check box in the future, however for now you can get around this by editing the header transformation using a *.mih file. Cheers, Dave