BSS run error on data type

Forums Forums BrainSuite Statistics toolbox (BSS) BSS run error on data type

This topic contains 6 replies, has 3 voices, and was last updated by  Anand Joshi 4 years ago.

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  • #127

    jiafucang
    Participant

    Hi,

    I am using BSS to do statistical analysis, but encountered a problem,
    The program runs on Windows 10 workstation, with Miniconda, R-3.2.2(x64) installed in the default location.
    When python bss_run.py modelspec_skeleton_cbm_left.ini ../output_cbm_left in D:\software\BrainSuite\USC2015\ICBM25, it outputs the following error info.

    Unexpected error: <type ‘exceptions.TypeError’>
    Traceback (most recent call last):
    File “bss_run.py”, line 82, in bss_run
    statsdata = StatsData(model.demographics, model)
    File “C:\Miniconda\lib\site-packages\bss\stats_data.py”, line 93, in __init__
    self.atlas_data = NimgDataio.read(model.atlas, attributes_only=False)
    File “C:\Miniconda\lib\site-packages\bss\nimgdata_io.py”, line 74, in read
    return NimgDataio.read_surface(filename)
    File “C:\Miniconda\lib\site-packages\bss\nimgdata_io.py”, line 88, in read_surface
    return dfsio.readdfs(filename)
    File “C:\Miniconda\lib\site-packages\bss\dfsio.py”, line 59, in readdfs
    NFV.faces = np.array(struct.unpack((‘i’ * 3 * hdr.nTriangles), fid.read(3 * hdr.nTriangles * 4)),
    TypeError: ufunc ‘multiply’ did not contain a loop with signature matching types dtype(‘S11’) dtype(‘S11’) dtype(‘S11’)
    None
    Elapsed time 0.0469999313354 sec.

    The modelspec_skeleton_cbm_left.ini is as follows:
    [subjectinfo]
    subjectid=subjID
    demographics=ICBM_demographics.csv
    fileid=File_cbm_left
    atlas=C:\Program Files\BrainSuite15b\svreg\BrainSuiteAtlas1\mri.left.mid.cortex.dfs
    maskfile=

    [analysis]
    type=cbm

    [model]
    modeltype=glm
    fullmodel=Age+Sex
    nullmodel=Sex
    test=anova

    Thank you very much!

    Best,
    Fcuang

  • #141

    David Shattuck
    Keymaster

    Hi Fcuang –

    We have a currently testing a fix for this. We will update you on this once it is ready for download.

    thanks,
    David Shattuck

  • #144

    David Shattuck
    Keymaster

    Hi Fcuang –

    The BSS software has been updated with a fix for this issue. Can you try reinstalling and let us know if it worked?

    thanks,
    David Shattuck

  • #145

    jiafucang
    Participant

    Hi David,

    Thank you very much, I updated to new version, and the problem is fixed. But I encounter some problem related to Miniconda packages, working on that. If the work is done, I will let you know.

    Best,
    Fucang

  • #148

    jiafucang
    Participant

    Hi David,

    The BSS works. Due to a patsy 0.4.0 version will give numeric error:
    Running the statistical model. This may take a while…
    Something went wrong. Please send this error message to the developers.
    Unexpected error: <type ‘exceptions.ValueError’>
    Traceback (most recent call last):
    File “bss_run.py”, line 89, in bss_run
    statsresult = statsengine.run()
    File “C:\Miniconda\lib\site-packages\bss\stats_engine.py”, line 88, in run
    statsresult = self.commands[self.model.analysis_type + ‘_’ + self.model.stat_test](self.model, self.stats_data)
    File “C:\Miniconda\lib\site-packages\bss\cbm_stats.py”, line 242, in anova_np
    X_design_full = dmatrix(model.fullmodel, data=sdata.demographic_data) # Design matrix for full model
    File “C:\Miniconda\lib\site-packages\patsy\highlevel.py”, line 278, in dmatrix
    NA_action, return_type)
    File “C:\Miniconda\lib\site-packages\patsy\highlevel.py”, line 152, in _do_highlevel_design
    NA_action)
    File “C:\Miniconda\lib\site-packages\patsy\highlevel.py”, line 57, in _try_incr_builders
    NA_action)
    File “C:\Miniconda\lib\site-packages\patsy\build.py”, line 706, in design_matrix_builders
    categories=None)
    File “C:\Miniconda\lib\site-packages\patsy\design_info.py”, line 88, in __init__
    raise ValueError(“For numerical factors, num_columns ”
    ValueError: For numerical factors, num_columns must be an int
    None
    Elapsed time 0.526000022888 sec.

    I updated the patsy to version 0.4.1

    Now it works great.

    Thank you very much!

    Best,
    Fucang

    • #210

      Anand Joshi
      Moderator

      Hi, It seems that the problems are fixed, but for the future, I recommend running
      >conda update –all
      after updating individual packages. This command will make sure that no dependencies are broken by the update.

  • #150

    David Shattuck
    Keymaster

    Fucang –

    Great! Glad to hear it’s working.

    cheers,
    David

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