Great tool! I’m testing Mindboggle out on a dataset that I have and with the existing documentation, have been able to run everything with relative ease. (Particularly helpful is the Docker container. Makes getting things up and running SUPER simple. Thank you for that).
I’m curious on how to visualize the various mesh outputs that mindboggle puts out. The viewer roygbiv is mentioned in several places but I’m unsure how to get it to run.
I’ve been able to successfully run a local server with the demo data, but am unsure how to import new data to visualize. Also, is roygbiv able to view non-summarized data? Meaning view measures (thickness, curv, etc) by vertex instead of by ROI?
To visualize mindboggle outputs with roygbiv, start your Docker image with:
docker run --rm -ti -v $HOST:$DOCK -p 5000:5000 --entrypoint /bin/bash nipy/mindboggle
and then inside the image, run
roygbiv /path/to/mindboggle_output_subject_folder and open a browser to localhost:5000.
Right now, roygbiv only shows summarized data, but I plan to add by-vertex visualizations in the future! In the meantime, check out paraview (https://www.paraview.org/).
Thank you, Anisha, and thank you for your interest, Eric!
I have added Anisha’s instructions to the mindboggle README:
Can you clarify more how this is suppose to work? I get the following error when I try to visualize the results:
Traceback (most recent call last):
File "/opt/conda/bin/roygbiv", line 31, in <module>
"please check that it exists and try again")
FileNotFoundError: [Errno Cannot find /home/jovyan/work/analyses/R21/mindboggled/003/exploded] please check that it exists and try again
I’m assuming I’m missing some part of the process since I do not have any subdirectories labeled
Oh I think I figured it out. Do you need to add the option
--roygbiv to your mindboggle code when you first run the analyses? You may want to put that in the instructions as well.
That’s correct – You need to include the flag --roygbiv to generate surface data that can be visualized with roygbiv. This flag is included by default when running mindboggle (via mindboggle123) with the docker run command, but not when running mindboggle independently. Thank you for alerting us to the lack of clarity in the documentation! I have added “–roygbiv” to examples in the README file and website (http://mindboggle.readthedocs.io/en/latest/).