BSS install issue

Forums Forums BrainSuite Statistics toolbox (BSS) BSS install issue

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    • #725
      alicemartini
      Participant

      Hi,

      I have a Macbook Air with MacOSX Sierra.

      I have a problem trying to install BSS. When I write the command /Application/BSS/bin/bss_prepare_data_for_tbm.py ~/Desktop/USC2015_BrainSuiteWorkshop/ICBM25 ICBM_demographics.csv modelspec_skeleton_tbm.ini -sigma 2.5

      The following error appear:
      -bash: /usr/local/lib/python3.6/site-packages/BSS/bin/bss_prepare_data_for_tbm.py: No such file or directory

      BSS is installed (I have checked via the upgrade command):

      MacBook-Air:~ myname$ pip install bss --upgrade
      Requirement already up-to-date: bss in /usr/local/lib/python2.7/site-packages
      Requirement already up-to-date: statsmodels>=0.6.1 in /usr/local/lib/python2.7/site-packages (from bss)
      Requirement already up-to-date: pandas>=0.19 in /usr/local/lib/python2.7/site-packages (from bss)
      Requirement already up-to-date: matplotlib>=1.5.3 in /usr/local/lib/python2.7/site-packages (from bss)
      Requirement already up-to-date: patsy>=0.4 in /usr/local/lib/python2.7/site-packages (from bss)
      Requirement already up-to-date: nibabel>=2.1 in /usr/local/lib/python2.7/site-packages (from bss)
      Requirement already up-to-date: numpy>=1.11 in /usr/local/lib/python2.7/site-packages (from bss)
      Requirement already up-to-date: scipy>=0.18 in /usr/local/lib/python2.7/site-packages (from bss)
      Requirement already up-to-date: python-dateutil in /usr/local/Cellar/matplotlib/2.0.2/libexec/lib/python2.7/site-packages (from pandas>=0.19->bss)
      Requirement already up-to-date: pytz>=2011k in /usr/local/lib/python2.7/site-packages (from pandas>=0.19->bss)
      Requirement already up-to-date: six>=1.10 in /usr/local/Cellar/matplotlib/2.0.2/libexec/lib/python2.7/site-packages (from matplotlib>=1.5.3->bss)
      Requirement already up-to-date: functools32 in /usr/local/Cellar/matplotlib/2.0.2/libexec/lib/python2.7/site-packages (from matplotlib>=1.5.3->bss)
      Requirement already up-to-date: subprocess32 in /usr/local/Cellar/matplotlib/2.0.2/libexec/lib/python2.7/site-packages (from matplotlib>=1.5.3->bss)
      Requirement already up-to-date: cycler>=0.10 in /usr/local/Cellar/matplotlib/2.0.2/libexec/lib/python2.7/site-packages (from matplotlib>=1.5.3->bss)
      Requirement already up-to-date: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=1.5.6 in /usr/local/lib/python2.7/site-packages (from matplotlib>=1.5.3->bss)

      Could you please help me to solve this issue?

      Thanks
      AM

    • #726
      shjoshi
      Moderator

      Hi Alice,

      If you installed bss using pip install bss, then I’m suspecting it must be installed in /usr/local/lib/python2.7/site-packages/bss or some such location.

      Did you move the bss folder to /Applications by any chance?

      I noticed you typed /Application/
      In the command you actually ran, I’m assuming you typed /Applications/ since that’s the correct folder name on Mac.

      Thanks,
      Shantanu

      PS: I should also let you know, that we are moving bss from python to R in the future. The release will happen before the end of this month. So if you were not in a rush to analyze the data, you could wait for the r package release. Just a thought.

    • #728
      alicemartini
      Participant

      Hi,

      many thanks for your prompt reply. You are right, bss is installed in /usr/local/lib/python2.7/site-packages/bss. However, there is no “bin” folder in it (and therefore the bss_prepare_data_for_tbm.py file).
      Unfortunately I need BSS soon to analyze my data.

      Best wishes,

      AM

    • #729
      shjoshi
      Moderator

      If bss is installed in /usr/local/lib/python2.7, then bss_prepare_data_for_tbm.py should go in the bin directory where you are calling python from. For e.g.
      /usr/local/bin, /usr/bin etc..

      you can do
      which pip
      or
      which python

      bss_prepare_data_for_tbm.py should be in the bin directory where your pip or python is located.

      S

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