BSS install issue

Forums Forums BrainSuite Statistics toolbox (BSS) BSS install issue

This topic contains 3 replies, has 2 voices, and was last updated by  shjoshi 2 years, 8 months ago.

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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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