[Neuroimaging] FmriRealign4d: TypeError: __init__() takes at least 4 arguments (7 given)

[Katie Surrence]

Thanks for the heads up!  Just upgrading nipype didn't work but I found a
page full of packages I was supposed to have (this one:
http://miykael.github.io/nipype-beginner-s-guide/installation.html) and I
upgraded all of them and now it works!  Sorry I wrote to the wrong list.

Thanks again,
Katie

On Mon, Aug 10, 2015 at 1:31 PM, Chris Filo Gorgolewski <
krzysztof.gorgolewski at gmail.com> wrote:

> Hi,
> Do you get the same error with the most up to date version of Nipype
> (0.10)?
>
> Best,
> Chris
>
> PS please use neurostars.org for user support next time.
>
> On Mon, Aug 10, 2015 at 10:26 AM, Katie Surrence <katiesurrence at gmail.com>
> wrote:
>
>> Dear Python neuroimagers,
>>
>> I'm brand new to NiPype, so excuse the very basic question.
>>
>> I am trying to use the FmriRealign4d algorithm.
>>
>> Based on the example here
>> <http://nipy.sourceforge.net/nipype/interfaces/generated/nipype.interfaces.nipy.preprocess.html>
>> I wrote the following to try to slice time correct/realign a single run:
>>
>> _____________________________
>>
>> from nipype.interfaces.nipy.preprocess import FmriRealign4d
>> import os
>>
>> pth = "/media/truecrypt1/SocCog/tmp1/run1L2"
>>
>> infile = os.path.join(pth, '4D.nii')
>>
>> realigner = FmriRealign4d()
>> realigner.inputs.in_file = [infile]
>> realigner.inputs.tr = 2.2
>> realigner.inputs.slice_order = range(0, 36, 2) + range(1, 35, 2)
>> realigner.inputs.time_interp = True
>> res = realigner.run()
>>
>>
>> _________________________________
>>
>>
>> (I added the explicit definition of time_interp because I got an error
>> when I didn't.)
>>
>> Here's the new error:
>>
>> _________________________________________
>>
>> /usr/local/lib/python2.7/dist-
>> packages/nipype-0.9.2-py2.7.egg/nipype/interfaces/base.py:376:
>> UserWarning: Input slice_order requires inputs: time_interp
>>   warn(msg)
>> Traceback (most recent call last):
>>   File "/home/katie/ks_scripts/python_scripts/pimriscripts/real4d.py",
>> line 17, in <module>
>>     res = realigner.run()
>>   File
>> "/usr/local/lib/python2.7/dist-packages/nipype-0.9.2-py2.7.egg/nipype/interfaces/base.py",
>> line 946, in run
>>     runtime = self._run_interface(runtime)
>>   File
>> "/usr/local/lib/python2.7/dist-packages/nipype-0.9.2-py2.7.egg/nipype/interfaces/nipy/preprocess.py",
>> line 162, in _run_interface
>>     start=self.inputs.start)
>> TypeError: __init__() takes at least 4 arguments (7 given)
>> Interface FmriRealign4d failed to run.
>>
>> Process finished with exit code 1
>>
>> _______________________________________+
>>
>>
>> I tried following the error in the debugger and it's going so deep into
>> such a complicated code base it seems very unlikely I'd be able to figure
>> it out.  Does anyone have any idea how to make this run?  I know it's
>> highly possible I'm doing something very obvious wrong.
>>
>> Thanks very much for your help.
>>
>> Best,
>> Katie
>>
>> --
>> Katie Surrence, M.S.
>> Research Coordinator
>> Social Cognition Laboratory
>> New York State Psychiatric Institute
>>
>> _______________________________________________
>> Neuroimaging mailing list
>> Neuroimaging at python.org
>> https://mail.python.org/mailman/listinfo/neuroimaging
>>
>>
>
> _______________________________________________
> Neuroimaging mailing list
> Neuroimaging at python.org
> https://mail.python.org/mailman/listinfo/neuroimaging
>
>


-- 
Katie Surrence, M.S.
Research Coordinator
Social Cognition Laboratory
New York State Psychiatric Institute
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