[pymvpa] Problems with 'preproc_fsl_ev.py'

[Michael Hanke]

Hi Matthias,

[ this message was probably intended for the PyMVPA mailing list.
  Therefore I am CC'ing both lists and doing a full quote. Let's move to
  the appropriate list -- 'Reply-to' is set accordingly. ]


On Wed, Jan 28, 2009 at 11:45:03AM +0100, Matthias Ekman wrote:
> Hi!
> 
> I have some problems concerning the preproc_fsl_ev.py example shipped 
> within the /doc/examples directory of pymvpa-0.4.0.
> (as far a I can see, there is no difference btw. preproc_fsl_ev.py in 
> pymvpa-0.4.0 and pymvpa-0.4.1)
> 
> Running the 'original' preproc_fsl_ev.py like:
> ./preproc_fsl_ev.py filtered_func_data.nii.gz ev1 ev1.txt
> 
> I'm getting this error:
> 
>   Loading data
>   Preprocess data
> Traceback (most recent call last):
>    File "./preproc_fsl_ev.py", line 123, in <module>
>      main()
>    File "./preproc_fsl_ev.py", line 89, in main
>      decimals = 0 ).astype('int') for ev in evs ]
> AttributeError: Values instance has no attribute 'tr'
> 
> Replace "options.tr" in line 88 with "opt.tr" and comment line 70 to 83, 
>   I'm getting this error with the 'modified' preproc_fsl_ev.py:
> 
>   Loading data
>   Preprocess data
> Traceback (most recent call last):
>    File "./preproc_fsl_ev.py", line 123, in <module>
>      main()
>    File "./preproc_fsl_ev.py", line 89, in main
>      decimals = 0 ).astype('int') for ev in evs ]
>    File "/var/lib/python-support/python2.5/nifti/utils.py", line 44, in 
> time2vol
>      vol = N.round( ( tmp + lag + tr/2 ) / tr, decimals )
> TypeError: unsupported operand type(s) for /: 'instance' and 'int'
> 
> 
> My ev-file is looking like this:
> 5.033	28	1
> 558.329	28	1
> 668.992	28	1
> 1222.255	28	1
> 1554.109	28	1
> 
> but even with a dummy ev-file like:
> 0	2	1
> 2	4	1
> 6	2	1
> 
> I'm getting the same error message.
> 
> Is it working for you? What am I missing here?
No, I guess it is broken for everyone.

Now let me start the excuse ;-)

You touched one of the ancient parts of PyMVPA that nobody has used for a
long time. At the same time this topic touches one of the most recent
additions to PyMVPA. In short: nothing in this broken script is needed
anymore and you have just triggered its removal.

Unfortunately, there is no comprehensive documentation about the 'new'
approach yet. I was working on this topic today and will continue with
it when I am done writing this email. However, this will take more than
a few days to finish.

In the meantime I can only provide you with a few pointers into the
module reference, so you might get an impression of how to proceed:


http://www.pymvpa.org/modref/mvpa.misc.fsl.base.html?highlight=event#mvpa.misc.fsl.base.FslEV3.toEvents

http://www.pymvpa.org/modref/mvpa.datasets.nifti.html?highlight=ernifti#mvpa.datasets.nifti.ERNiftiDataset


Cheers,

Michael


-- 
GPG key:  1024D/3144BE0F Michael Hanke
http://apsy.gse.uni-magdeburg.de/hanke
ICQ: 48230050