NITRC CBS High-Res Brain Processing Tools Forum: help

RE: installation problems

Pierre-Louis Bazin — Mon, 29 Jul 2024 7:53:32 GMT

<p>See above: I recommend you to switch to the Nighres python package, which includes most of the CBSTools software and more. We no longer maintain compatibility with JIST and MIPAV.</p>

RE: installation problems

Ajay Kumar H — Wed, 24 Jul 2024 6:58:38 GMT

<p>I got same error " Unable to load plugin"</p>

RE: installation problems

Pierre-Louis Bazin — Fri, 04 Feb 2022 8:19:26 GMT

Hi,

I have managed to install CBSTools over MIPAV 11 on linux, but there might be different issues on Mac. As mentioned earlier, CBSTools is no longer actively developed as a MIPAV plugin, due in large part to these installation problems. Nighres should be easier to work with, and includes almost all of the CBSTools functions (and many new ones). It is worth switching over (and you can interface easily with python toolboxes too). MIPAV remains an excellent data viewer and processing tool, but keeping up with both systems is a bit too much for us.

RE: installation problems

Heather Robinson — Thu, 03 Feb 2022 19:21:54 GMT

Hello,

I also had this same plugin installation problem with MIPAV 11 and tried to install MIPAV 8.1 instead, but it is not compatible with my current Mac OS (Monterey).

Are these plugins compatible with any other recent MIPAV versions? If not, do you know what the most recent Mac OS is compatible with MIPAV 8.1? Alternatively, would you recommend using Nighres if we cannot get MIPAV to work?

Thanks in advance!

RE: Failed modules

alicianorthall — Mon, 15 Jun 2020 8:58:04 GMT

We need TOADS-CRUISE. Do you know if cbs tools is running on mipav version 10?

RE: Failed modules

Pierre-Louis Bazin — Wed, 10 Jun 2020 8:17:12 GMT

What modules are you missing? We tried to port all the ones needed for 7T, but if there's something missing we'd like to know!

RE: Failed modules

alicianorthall — Tue, 09 Jun 2020 11:07:25 GMT

OK, that explains why modules fail for only some subjects. I get this error in the debugging info for the modules that fail (attached screenshot).

I plan to set up Nighres but it does not currently support all of the algorithms I need.

RE: Failed modules

Pierre-Louis Bazin — Thu, 04 Jun 2020 11:43:29 GMT

Yes, memory is likely the culprit here. Note that several steps attempt to reduce memory usage based on the parts of the image that need to be processed, so the limit can vary from subject to subject. And of course other activities on your computer might limit further the amount of memory you can allocate to Java.

As a note, many of the CBSTools have been ported to Nighres, a python-based library with a slightly smaller memory footprint.

Failed modules

alicianorthall — Wed, 03 Jun 2020 10:55:14 GMT

Hello,

I'm using MIPAV 7.3.0 and CBS tools 3.0.8 on Mac desktop 10.14.6 (Mojave) - I am avoiding upgrading to Catalina! My computer has 16GB RAM and i work with 0.4mm images.

When running ANTS 1.9x to register an 0.4mm image to a 0.7mm image, the module sometimes fails even after processing for a whole day. Now I am experiencing the same problem when running TOADS-CRUISE on a merged image (of the two resolutions). For some subjects, TOADS runs successfully after 1h30-3h but for some it fails. Do I need to use a computer with higher RAM? The cbs tools guide recommends using 15-24GB RAM for high resolution data. Although this seems unlikely given that it works for some subjects.

I have attached a screenshot of the error I get in the terminal when the TOADS module fails.

Thanks,
Alicia

RE: installation problems

Pierre-Louis Bazin — Tue, 02 Jun 2020 6:41:50 GMT

Hi there,

the installation has not been tested with the most recent versions of MIPAV, you might have better luck with MIPAV 8.1. Note also that the CBSTools toolbox has been integrated into the python toolbox Nighres, which is much simpler to install and interface with other software.