shjoshi

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Viewing 15 posts - 16 through 30 (of 34 total)
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  • in reply to: Unable to install BSS #875
    shjoshi
    Moderator

    Thanks. I recon this is due to the file separators on Windows.
    Can you please do the following?

    1. Can you run
    check_file_exists(“D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/2011101206/2011101206.svreg.log”)

    2. Attach/paste the contents of the file 2011101206.svreg.log

    3. Run get_brainsuite_install_path()

    4. get_brainsuite_atlas_id_from_logfile(“D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/2011101206/2011101206.svreg.log”)

    in reply to: Unable to install BSS #873
    shjoshi
    Moderator

    Hmm. Can you do one more thing?
    Type these 3 commands:

    file.path(‘D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/’, “2011101206”, ‘*.svreg.log’)

    Sys.glob(file.path(‘D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/’, “2011101206”, ‘*.svreg.log’))

    check_file_exists(Sys.glob(file.path(‘D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/’, “2011101206”, ‘*.svreg.log’)))

    in reply to: Unable to install BSS #868
    shjoshi
    Moderator

    Hi Tetsuya,

    Does the path D:/Tetsuya/All_data/MRI/DTIandMPRAGE/38NC/2011101206 actually exist on disk?

    I.e. Does the directory DTIandMPRAGE exist in the directory MRI?
    Or did you just change & to and in the command?

    Thanks,
    Shantanu

    in reply to: Unable to install BSS #864
    shjoshi
    Moderator

    Hm.. Is this because of the “&” in the file name?
    In RStudio, what does
    dir(“D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/2011101206/2011101206.svreg.log”)
    give you?

    Please not the quotes “” above may not be correctly formatted online. Please don’t copy the command as is, but type in the start and the end quotes.

    • This reply was modified 4 years, 2 months ago by shjoshi.
    • This reply was modified 4 years, 2 months ago by shjoshi.
    in reply to: Unable to install BSS #863
    shjoshi
    Moderator

    Hm.. Is this because of the “&” in the file name?
    In RStudio, what does
    dir(‘D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/2011101206/2011101206.svreg.log’)
    give you?

    in reply to: Unable to install BSS #860
    shjoshi
    Moderator

    Hi Tetsuya,

    A couple of things…
    1. Is the “&” in your path creating this problem?
    2. Does your path start with D, or is this D:/ ?

    Also you could run the stats on the command line, but I would suggest running it through RStudio. It’s easier and you can do this step by step.

    I’ve added tutorial slides in the bottom at http://brainsuite.org/bssr/ for standard usage cases.

    Shantanu

    in reply to: Unable to install BSS #825
    shjoshi
    Moderator

    Glad to know the installation worked out.

    in reply to: Unable to install BSS #822
    shjoshi
    Moderator

    Hi Tetsuya,

    We have now ported BSS to R. You can find the link at http://brainsuite.org/bssr
    The instructions to install are much simpler and should work for you on Windows.
    Can you please give it a try?

    Thanks,
    Shantanu

    in reply to: BSS install issue #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

    in reply to: BSS install issue #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.

    in reply to: Problem running bss_run.py -h script #560
    shjoshi
    Moderator

    Hello,

    It seems even if you invoked install.sh with sudo, some of the installation files were not written to /usr/share.

    Can you actually try installing bss in your user or home directory, where you don’t need sudo?

    in reply to: Problem running bss_run.py -h script #393
    shjoshi
    Moderator

    Hmm. is it possible to paste the entire error including the output on the screen when you run the installation command?

    Thanks,
    Shantanu

    in reply to: Unable to install BSS #356
    shjoshi
    Moderator

    Yes, we are trying to work on it. Some packages cannot be compiled from source on Windows very easily so we need to make the binaries available. This makes the installation process complicated.

    We are hoping that with the release of the new bash shell in Windows 10, the installation process may become easier.

    Thanks,
    Shantanu

    in reply to: Mapping of multiple subjects to Common Atlas Space #348
    shjoshi
    Moderator

    Hi Alexander,

    I was wondering if you can repost this message in the SVREG forum (http://forums.brainsuite.org/forums/forum/svreg/)

    This is directly seen by the svreg developers who will be able to answer your question.

    Thanks,
    Shantanu

    in reply to: Problem running bss_run.py -h script #347
    shjoshi
    Moderator

    Hi Dr. Neyaz,

    We have now made the installation process on Linux/Mac much simpler.
    The new instructions are located at
    http://brainsuite.org/bss/bss-download/

    Essentially you just have to download the install.sh script and run it as:

    bash install.sh <full path to the bss installation directory>

    The above problem will have been fixed in this version.

    Thanks,
    Shantanu

Viewing 15 posts - 16 through 30 (of 34 total)