Debugging use of PyMVPA BIDS app

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Hi. I am attempting to use the following BIDS app for MVPA analysis of

I have successfully gone through step 1. The data I am working with have been preprocessed using fmriprep. I have also created a mask according to the method specified on that page. Has anyone run into a similar error? If so, have you been able to debug it? I am wondering if there is something wrong with the data I am working with, the mask that I have used, or the code.

I currently have the error: (base) wifi-roaming-128-4-168-23:PyMVPA-master Stefan$ python2 run_edited2.py -k asl -c struct rand --skip_bids_validator /Users/Stefan/data/bids /Users/Stefan/data/bids/outputs1 participant_test
/Library/Python/2.7/site-packages/mvpa2/testing/tools.py:81: DeprecationWarning: Importing from numpy.testing.decorators is deprecated since numpy 1.15.0, import from numpy.testing instead.
from numpy.testing.decorators import skipif
WARNING: Detected incorrect (nan) scl_ fields. Resetting to scl_slope=1.0 and scl_inter=0.0
* Please note: warnings are printed only once, but underlying problem might occur many times *
Traceback (most recent call last):
File “run_edited2.py”, line 280, in
fds.sa[‘chnks’] = chunks_labels # we call this sample attribute ‘chnks’ so later it won’t be mistaken for
File “/Library/Python/2.7/site-packages/mvpa2/base/collections.py”, line 599, in setitem
str(self)))
ValueError: Collectable ‘chnks’ with length [3840] does not match the required length [1920] of collection ‘<SampleAttributesCollection: time_coords,time_indices>’.

Thanks much,
Stefan Bartell
graduate student, University of Delaware
https://sites.udel.edu/q-lab/

2

Hi Stefan, You posted this a long time ago and I hope the issue was solved, but for future please include the “pymvpa” tag in your post, otherwise we might miss your question.

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P.S. If this is still an issue, please include the related part of your code. As the error message says, this is happening because you have 1920 time points (samples) in your data while chunks_labels has 3840 elements, which cannot be attributed to your fds dataset as their length don’t match.