Error with realign( )

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1

Hi,
Im trying to learn to preprocess fmri data using nipype.
Before I learn to use nodes workflows etc. I call everything like in the following (running through all my functional niftii files:

realigner.inputs.in_files = niftii files
realigner.inputs.register_to_mean = True

realigner.run()

It results in the correct output and finishes the job. Although it produces the following comment:
stty: standard input: Invalid argument. Repeating this throughout this preprocessing step. Im just wondering why this is the case?

Btw:
In preprocessing with Nipype, are there tools that enables information about how well the preprocessing step when, that produces graphs of motioncorrection etc.?

2

I’m guessing that you’re using Realign() from spm, but can you please confirm and show how are realigner and nifti files defined.

Can’t really replicate your standard input error with Realign(). Do you have this issue with other interfaces?

3

Using the following:
from nipype.interfaces.spm import Realign

realigner = Realign( )

I have a list (=infiles) containing the directory to the niftifiles. Followed by,

realigner.inputs.in_files = infiles
realigner.inputs.register_to_mean = True

realigner.run( )

Appreciate your reply

4

Just to clarify, in_files has to be a lists of files not directories.

can you please paste entire output of the realiner.run()