[pymvpa] Chnks length error using bids/pymvpa

[John Johnson]

My data were previously processed with fmriprep.
I’ve used the participant_prep on my subjects, resampled my masks, 
both successful. However, when I attempt participant_test, I receive an 
error that the chnk[sic] length is incorrect. If I select individual 
participants, the number can change (despite the protocol being the same 
for everyone). Each subject has one session of four runs of 238 volumes 
each, for a total of 952 volumes. The chnk length is always a multiple 
of 238, but not 952 as it should be (I think). It is sometimes 1904, or 
2856, etc.

For each subject I ran
`./mvpa 01` etc. for each subject 01-15, which ran the script:
```
docker run -i --rm \
	-v /Users/john/CloudStation/School/Research/fmri/aim1:/data:ro \
	-v 
/Users/john/CloudStation/School/Research/fmri/aim1/derivatives/pymvpa:/outputs 
\
	bids/pymvpa \
	--skip_bids_validator \
	/data /outputs participant_prep -k ao -p $*
```

Then ran:
`./mvpa2 -c altdev famsalt famssame intalt intsame` which calls the 
following script:

```
#!/bin/bash

docker run -i --rm \
	-v /Users/john/CloudStation/School/Research/fmri/aim1:/data:ro \
	-v 
/Users/john/CloudStation/School/Research/fmri/aim1/derivatives/pymvpa:/outputs 
\
	bids/pymvpa \
	--skip_bids_validator \
	/data /outputs participant_test -k ao $*
```

Which produced deprecation warnings and the following error:

```
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 "/code/run.py", line 281, in <module>
     fds.sa['chnks'] = chunks_labels  # we call this sample attribute 
'chnks' so later it won't be mistaken for
   File "/usr/lib/python2.7/dist-packages/mvpa2/base/collections.py", 
line 599, in __setitem__
     str(self)))
ValueError: Collectable 'chnks' with length [2856] does not match the 
required length [952] of collection '<SampleAttributesCollection: 
time_coords,time_indices>'.
```

I would greatly appreciate any help or pointers to online info.

John T. Johnson
PhD Candidate - Cognitive Motor Control Laboratory
Lab TA NEURO 4001 Capstone
School of Biological Sciences
Georgia Institute of Technology

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