Unable to install BSS

Forums Forums BrainSuite Statistics toolbox (BSS) Unable to install BSS

This topic contains 25 replies, has 4 voices, and was last updated by  iidaka 3 months ago.

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  • #286

    zafarneyaz
    Participant

    Hi,

    I am working on a Intel ®core ™i7-3770 CPU 3.4 GHz, 8GB RAM, with window 7 professional installed.

    Brainsuite15b, Matlab complier 12b, visual basics are installed. Brain extraction, SV reg and BPD are working.

    To work on statistics part…I installed R-3.2.2-win.exe, Miniconda-latest-Windows-x86_64.exe downloaded from brainsuite website.

    Both programs are located in C:\ProgramFiles folder.

    Then I run BSS_Install.bat with Command Prompt (Admin). It installs many files and except for few messages, all soft wares are successfully installed.

    >> Setting R Environment to c:\Program Files\R\R-3.2.2\bin\x64\

    WARNING: The data being saved is truncated to 1024 characters.

    >> Error in read.dcf(file.path(pkgname, “DESCRIPTION”), c(“Package”, “Type”)) :

    cannot open the connection

    Ultimately the program is installed:

    Running setup.py install for bss … done

    Successfully installed bss-0.1.dev0

    BSS Install Successfully

    Press any key to continue . . .

    • However… there is no bss folder in brainsuite program folder. bss folder is located in miniconda folder { C:\Program Files\Miniconda\Lib\site-packages\bss }. There is no bin in bss folder. I have tried running python bss_run.py –h from this folder as well as from {C:\Program Files\Miniconda\Scripts }. But it is not working. Please help me, I am stuck at this step.

  • #288

    shjoshi
    Moderator

    Hello,

    This is the correct installation behavior. BSS will not install in the BrainSuite program folder, but will be installed in the Scripts\ directory.

    Now there is some issue in setting the PATH where you get the warning,
    “WARNING: The data being saved is truncated to 1024 characters.”

    Can you check if these paths are correctly set?

    Can you also post the output of python bss_run.py -h

    Thanks,
    Shantanu

  • #289

    zafarneyaz
    Participant

    Hi,
    There is no folder named as “directory or “bin” in the scripts folder. However, there is a file in scripts folder named “bss_run.py”. When I try to run the command “python bss_run.py –h” from this folder, the following message comes.

    C:\Users>cd C:\Program Files\Miniconda\Scripts
    C:\Program Files\Miniconda\Scripts> python bss_run.py -h
    Error: DLL load failed: The specified module could not be found.
    Something happened during imports.
    Perhaps R is not installed properly or R_HOME is not setto the correct version
    Please send the whole message to the developers.
    C:\Program Files\Miniconda\Scripts>

    I have already posted the warning messages during the installation process.
    1. Setting R Environment to c:\Program Files\R\R-3.2.2\bin\x64\
    WARNING: The data being saved is truncated to 1024 characters.
    2. Error in read.dcf(file.path(pkgname, “DESCRIPTION”), c(“Package”, “Type”)) :
    cannot open the connection

    I am a radiologist and less familiar with computer commands.

    Dr. Zafar Neyaz
    Associate Professor
    Dept. of Radiodiagnosis
    SGPGIMS, Lucknow , U.P. – India

  • #291

    shjoshi
    Moderator

    Hi Dr. Neyaz,

    Looks like the programs are installed but the paths are not set correctly. This relates to the warning of 1024 character path lengths on Windows 7, “WARNING: The data being saved is truncated to 1024 characters.”

    Incidentally we have not tested BSS on Windows 7. Just wondering if it’s possible to upgrade your OS to a later version?

    Thanks,
    Shantanu

  • #328

    iidaka
    Participant

    Hi experts,

    The same trouble is happening on my Windows7 PC.
    Warning message is the same as above.

    Will it be fixed soon?

    Regards,

    Tetsuya

  • #329

    shjoshi
    Moderator

    Dear users,

    Bss was tested on Windows 8 and 10. We are currently in the process of getting access to a Windows 7 machine to test these installation problems. Please stay tuned.

    Thanks,
    Shantanu

  • #355

    zafarneyaz
    Participant

    Please provide a single line command for installation of all components of bss for windows 7 /10, so that less experienced uses may install it

  • #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

  • #588

    geming
    Participant

    Hi,

    It seems that 1024 truncation problem also exists on win 10. Does anyone have a solution for it ?

    Thanks

    GM

  • #810

    iidaka
    Participant

    Hi, experts,

    I am using BrainSuite 17a on Windows10 and still unable to install BSS.
    There is no bss folder.

    Best regards,

    tetsuya

  • #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

  • #824

    iidaka
    Participant

    Hi, Shantanu

    Thank you for response.

    The installation has completed successfully.
    I will try my data and report it.

    Best regards,

    tetsuya

  • #825

    shjoshi
    Moderator

    Glad to know the installation worked out.

  • #858

    iidaka
    Participant

    Hi,

    I have encountered following error.

    Regards,

    Tetsuya

    *******************************
    bss_cbm_anova.R –subjdir=D/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC –csv=D/Tetsuya/All_data/MRI/DTI&MPRAGE/NC38.csv –hemi=left –main_effect=gender –covariates=age –odir=D/Tetsuya/All_data/MRI/DTI&MPRAGE/NC38_gender_sex –smooth=2.5

    Error: unexpected symbol in “bss_cbm_anova.R –subjdir=D/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC

  • #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

  • #862

    iidaka
    Participant

    Hi,

    Thank you for instruction for bssr. There is another error message like this.

    ****
    Error: Could not determine the BrainSuite atlas used for registration.
    Please check the log file D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/2011101206/2011101206.svreg.log, and check if the subject directory is valid. If using a custom atlas, supply the path in the atlas= argument.
    ****

    In avreg.log file, there is a path to the atlas like this.
    C:\Program Files\BrainSuite17a\svreg\BrainSuiteAtlas1\mri

    Best regards,

    tetsuya

  • #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?

  • #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 3 months, 1 week ago by  shjoshi.
    • This reply was modified 3 months, 1 week ago by  shjoshi.
  • #867

    iidaka
    Participant

    Hi,

    Your script gives “character(0)”

    If “&” was replaced by “and” the error message is the same as before.

    **************************
    Error: Could not determine the BrainSuite atlas used for registration.
    Please check the log file D:/Tetsuya/All_data/MRI/DTIandMPRAGE/38NC/2011101206/2011101206.svreg.log, and check if the subject directory is valid. If using a custom atlas, supply the path in the atlas= argument

  • #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

  • #872

    iidaka
    Participant

    Hi,

    This path really exists on my PC. It is working in previous directory.

    I am afraid that “Yen mark” instead of “/” is used to separate directry in
    Japanese PC and svreg.log file uses Yen mark.

    *********************
    > dir(“D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/2011101206/”)
    [1] “2011101206.air” “2011101206.bfc.nii.gz”
    [3] “2011101206.brain.dfs” “2011101206.bse.nii.gz”
    [5] “2011101206.bval” “2011101206.bvec”
    [7] “2011101206.cerebrum.mask.nii.gz” “2011101206.cortex.dewisp.mask.nii.gz”
    [9] “2011101206.cortex.scrubbed.mask.nii.gz” “2011101206.cortex.tca.mask.nii.gz”
    [11] “2011101206.hemi.label.nii.gz” “2011101206.init.cortex.mask.nii.gz”
    [13] “2011101206.inner.cortex.dfs” “2011101206.inner_skull.dfs”
    [15] “2011101206.left.inner.cortex.dfs” “2011101206.left.inner.cortex.svreg.dfs”
    [17] “2011101206.left.mapped.dfc” “2011101206.left.mid.cortex.svreg.dfs”
    [19] “2011101206.left.mid.cortex.svreg.init.dfs” “2011101206.left.pial.cortex.dfs”
    [21] “2011101206.left.pial.cortex.svreg.dfs” “2011101206.mask.nii.gz”
    [23] “2011101206.nii” “2011101206.outer_skull.dfs”
    [25] “2011101206.pial.cortex.dfs” “2011101206.pvc.frac.nii.gz”
    [27] “2011101206.pvc.label.nii.gz” “2011101206.right.inner.cortex.dfs”
    [29] “2011101206.right.inner.cortex.svreg.dfs” “2011101206.right.mapped.dfc”
    [31] “2011101206.right.mid.cortex.svreg.dfs” “2011101206.right.mid.cortex.svreg.init.dfs”
    [33] “2011101206.right.pial.cortex.dfs” “2011101206.right.pial.cortex.svreg.dfs”
    [35] “2011101206.roiwise.stats.txt” “2011101206.roiwise.stats.xlsx”
    [37] “2011101206.scalp.dfs” “2011101206.skull.label.nii.gz”
    [39] “2011101206.svreg.init.label.nii.gz” “2011101206.svreg.inv.jacobian.nii.gz”
    [41] “2011101206.svreg.inv.map.nii.gz” “2011101206.svreg.jacobian.nii.gz”
    [43] “2011101206.svreg.label.nii.gz” “2011101206.svreg.log”
    [45] “2011101206.svreg.map.nii.gz” “2011101206.warp”
    [47] “2011101206diff.nii” “atlas.left.mid.cortex.jacobian.dfs”
    [49] “atlas.left.mid.cortex.svreg.dfs” “atlas.right.mid.cortex.jacobian.dfs”
    [51] “atlas.right.mid.cortex.svreg.dfs” “brainsuite_labeldescription.xml”
    [53] “dicom”

    > dir(“D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/2011101206/2011101206.svreg.log”)
    character(0)
    >

  • #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’)))

  • #874

    iidaka
    Participant

    Hi,

    The first,
    [1] “D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC//2011101206/*.svreg.log”
    The second,
    character(0)
    The third,
    [1] FALSE

  • #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”)

  • #876

    iidaka
    Participant

    Sorry, the results in previous mail was incorrect.

    The first
    [1] “D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC//2011101206/*.svreg.log”

    The second
    [1] “D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC//2011101206/2011101206.svreg.log”

    The third
    [1] TRUE

  • #877

    iidaka
    Participant

    This is a reply to the last mail.

    1.
    [1] TRUE

    2.
    svreg_label_surf_hemi D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206 C:\Program Files\BrainSuite17a\svreg\BrainSuiteAtlas1\mri right -v1
    svreg_label_surf_hemi D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206 C:\Program Files\BrainSuite17a\svreg\BrainSuiteAtlas1\mri left -v1
    register_cc_curve D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206.svreg.tmp\2011101206.right.mid.cortex_smooth10.dfs
    register_cc_curve D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206.svreg.tmp\2011101206.left.mid.cortex_smooth10.dfs
    volmap_ball D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206.svreg.tmp\2011101206.target 1 -v1
    volmap_ball D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206 1 -v1
    svreg_volreg D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206 D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206.target -v1
    refine_ROIs2 D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206 left refine_ROIs2 D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206 right -v1 -v1
    svreg_refinements D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206 D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206.target -v1
    generate_stats_xls D:\Tetsuya\All_data\MRI\DTI&MPRAGE\38NC\2011101206\2011101206 -r

    3.
    [1] “C:/Program Files/BrainSuite17a”

    4.
    Error: Could not determine the BrainSuite atlas used for registration.
    Please check the log file D:/Tetsuya/All_data/MRI/DTI&MPRAGE/38NC/2011101206/2011101206.svreg.log, and check if the subject directory is valid. If using a custom atlas, supply the path in the atlas= argument.

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