SPM examples incorrect

[thomas.nickson]

Hey I don't know if this is the best place for it but I tried running some of the spm examples and in fact basing some of my own pipelines on the examples provided and I don't think that they are correct. At least they don't work for me.

In the following pipelines:

http://nipy.sourceforge.net/nipype/users/examples/fmri_spm_auditory.html
http://nipy.sourceforge.net/nipype/users/examples/fmri_spm_face.html

There is code like this but it never worked for me. The indicated lines are the problem

preproc.connect([(realign,coregister,[('mean_image', 'target')]),
                 (coregister, segment,[('coregistered_source','data')]),
                 (segment, normalize_func, [('transformation_mat','parameter_file')]),
                 (segment, normalize_struc, [('transformation_mat','parameter_file'),
                                             ('modulated_input_image', 'apply_to_files'),<------------------------------
                                             (('modulated_input_image', get_vox_dims), 'write_voxel_sizes')]),<-------------------
                 (realign, normalize_func, [('realigned_files', 'apply_to_files'),
                                            (('realigned_files', get_vox_dims), 'write_voxel_sizes')]),
                 (normalize_func, smooth, [('normalized_files', 'in_files')]),
                 ])

I think they should be replaced with

preproc.connect(coregister,'coregistered_source', normalize_struc, 'apply_to_files')

This is the method used in the spm manual anyway. I'm not even sure what the modulated_input_image is but it always crashed out.

Thanks.

[Satrajit Ghosh]

hi thomas,

fmri_spm_face should be fine it uses the appropriate output name (bias_corrected_image). could you please submit an issue on github?

those examples were meant to mimic the tutorials. it's been a long while since we ran them. 

cheers,

satra

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[Thomas Nickson]

Okay, I'll try running the code as it's provided with some of the data next week. It doesn't fit the work flow of the manual though. When I altered to mimic that everything worked fine.

Thanks,

Tom

[Satrajit Ghosh]

hi tom,

please feel free to submit a PR to reflect changes in the manual - some of the code originates from 4-5 years back and we weren't as careful in reviewing code then.

cheers,

satra

[Thomas Nickson]

What is a PR?

[Chris Filo Gorgolewski]

It's a pull request: https://help.github.com/articles/using-pull-requests

It's a very easy way to submit improvements to github projects. Looking forward to your contribution!

Best,

Chris