error with multiple but not single runs - rsfmri_fsl_compcorr

[Cris Lanting]

Dear all,

I've been trying to set-up a nipype pipeline to analyze resting state data (based on http://nipy.org/nipype/users/examples/rsfmri_fsl_compcorr.html)

If I run the pipeline with one file ('rs1.nii') over multiple subjects ('subject1','subject2') it works like a charm, but if I want to extend it to multiple runs it fails.

This works:

subject_list = ['subject1','subject2']

infosource = pe.Node(interface=util.IdentityInterface(fields=['subject_id']),

                     name="infosource")

infosource.iterables = ('subject_id', subject_list)

datasource = pe.Node(interface=nio.DataGrabber(infields=['subject_id'],

                                               outfields=['func', 'struct']),

                     name = 'datasource')

datasource.inputs.base_directory = data_dir

datasource.inputs.template = '%s/%s.nii'

# Map field names to individual subject runs.

info = dict(func=[['subject_id', ['rs1']]])

But it fails if I alter the last line into:

info = dict(func=[['subject_id', ['rs1','rs2']]])

It then gives the following error:

TraitError: The 'in_file' trait of a SliceTimerInputSpec instance must be an existing file name, but a value of ['/Users/crislanting/Projects/RestingState/rest/subject2/rs1.nii', '/Users/crislanting/Projects/RestingState/rest/subject2/rs2.nii'] <type 'list'> was specified.

If I look at other examples (e.g., http://nipy.org/nipype/_downloads/fmri_spm.py) it seems it would be fine to define the files the way I did (in a list):

info = dict(func=[['subject_id', ['f3','f5','f7','f10']]],i
            struct=[['subject_id','struct']])

Is there something missing like an iterable over runs or is it something peculiar about traits?

Additionally, is there a simple way to disable the slice-timing as the data is acquired using sparse-sampling (TR = 12 s with a silent ISI of 10 s)? 

(referring to "from nipype.workflows.fmri.fsl import create_resting_preproc")

Cheers,

Cris

[Satrajit Ghosh]

hi chris,

all the nodes in that workflow are regular nodes.

https://github.com/nipy/nipype/blob/b1b78251dfd6f3b60c6bc63f79f86b356a8fe9cc/nipype/workflows/rsfmri/fsl/resting.py#L127

you would have to rewrite that function using MapNodes at appropriate places.

cheers,

satra

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[Cris Lanting]

Thanks Satra - a good nudge in the right direction! http://nipy.org/nipype/users/mapnode_and_iterables.html is also quite helpful in retrospect...

I've also (at least conceptually) figured out how to get rid of the slice-timing node.

Cheers,

Cris