[jiafucang]

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

[David Shattuck]

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

[David Shattuck]

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

[jiafucang]

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

[jiafucang]

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

[Anand Joshi]

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.

[David Shattuck]

Fucang –

Great! Glad to hear it’s working.

cheers,
David

[Author]

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