FmriRealign4d without slice timing correction

[Philipp Ehses]

Hello,

I'm having trouble running FmriRealign4d without slice timing correction as a nipype-node. With slice timing correction, everything works fine.

In the nipype interface documentation, it says that the input 'time_interp' should be set to undefined:

time_interp: (True)
Assume smooth changes across time e.g., fmri series. If you don't
want slice timing correction set this to undefined
requires: slice_order

First, this is a little misleading since the InputSpec-Trait only allows the value 'True' (so setting it to traits.trait_base _Undefined will result in an error). Second, not setting time_interp does work as intended (i.e. time_interp == _Undefined), however running the interface then fails with the following message:

TypeError: '_Undefined' object is not iterable
Interface FmriRealign4d failed to run.


Cheers,

Philipp

[Satrajit Ghosh]

hi philipp,

which version of nipype and nipy are you using (nipype/nipy.get_info())? 

In the nipype interface documentation, it says that the input 'time_interp' should be set to undefined:

time_interp: (True)
Assume smooth changes across time e.g., fmri series. If you don't
want slice timing correction set this to undefined
requires: slice_order

First, this is a little misleading since the InputSpec-Trait only allows the value 'True' (so setting it to traits.trait_base _Undefined will result in an error).

Undefined is special in this sense, and you should try to set it with:

from nipype.interfaces.base import Undefined

 

Second, not setting time_interp does work as intended (i.e. time_interp == _Undefined), however running the interface then fails with the following message:

TypeError: '_Undefined' object is not iterable
Interface FmriRealign4d failed to run.

the current master is broken in this aspect. if you have the last nipy release 0.2 that should work fine. there is a pull-request in place to fix this in nipy.

https://github.com/nipy/nipy/pull/232

cheers,

satra

[Philipp Ehses]

Hi Satra,

thanks again for the quick reply. Ok, setting time_interp to Undefined works now.

Yes, I'm (was) running the current master. And you're right, I just tried it with the nipy release from neurodebian (0.2) and it works!

Cheers,

Philipp