BRAINSTools installation fails

[jhlegarreta]

Following the instructions in https://github.com/pnlbwh/pnlpipe/tree/master#4-installing-software-without-using-pipeline to install BRAINSTools yields the following error:

Traceback (most recent call last):
  File "./pnlpipe", line 10, in <module>
    import pnlpipe_cli.pipecmd
  File "/home/jhlegarreta/src/pnlpipe/pnlpipe_cli/__init__.py", line 3, in <module>
    from .caseidnode import *
  File "/home/jhlegarreta/src/pnlpipe/pnlpipe_cli/caseidnode.py", line 3, in <module>
    from pnlpipe_software import BRAINSTools, trainingDataT1AHCC, FreeSurfer
ImportError: cannot import name 'BRAINSTools' from 'pnlpipe_software' (unknown location)

Happened while trying to do this:

Feel free to try it and submit PR if https://github.com/pnlbwh/pnlpipe/tree/master#tests pass.

Ubuntu 22.04 LTS. Python 3.8.

[tashrifbillah]

1. BRAINSTools is no longer used. We needed this for ConvertBetweenFileFormats and DWIConvert. We replaced those commands with https://github.com/pnlbwh/conversion . So no need to be sad about it.

2. It failed more often than not. You may contact BRAINTools people if you have a dire need for this.

3. Or you can use https://github.com/pnlbwh/pnlpipe-containers where we built everything for you.

Good luck.

[jhlegarreta]

If it is no longer used, then updating the installation instructions would be of great benefit.