fMRI pipeline doesn't work from commandline

[ncullen93]

When I try to run the fMRI pipeline directly from the commandline -- connectomemapper sub_dir sub_dir/fMRI_config.ini -- it doesn't seem to convert the fMRI dicom images from RAWDATA into NIFTI, and it gives me this error:

Inputs check finished successfully.
Diffusion and morphological data available.
/thayerfs/home/f002b6j/.local/lib/python2.7/site-packages/nipype/interfaces/base.py:359: UserWarning: Input apply_xfm requires inputs: in_matrix_file
warn(msg)
/thayerfs/home/f002b6j/.local/lib/python2.7/site-packages/nipype/interfaces/base.py:359: UserWarning: Input apply_xfm requires inputs: in_matrix_file
warn(msg)
Traceback (most recent call last):
File "/thayerfs/home/f002b6j/.local/bin/connectomemapper", line 87, in
pipeline.process()
File "/thayerfs/home/f002b6j/.local/lib/python2.7/site-packages/cmp/pipelines/diffusion/diffusion.py", line 259, in process
reg_flow = self.create_stage_flow("Registration")
File "/thayerfs/home/f002b6j/.local/lib/python2.7/site-packages/cmp/pipelines/common.py", line 141, in create_stage_flow
stage.create_workflow(flow,inputnode,outputnode)
File "/thayerfs/home/f002b6j/.local/lib/python2.7/site-packages/cmp/stages/registration/registration.py", line 216, in create_workflow
(fsl_applyxfm_eroded_wm, outputnode, [('out_file','eroded_wm_registered')])
File "/thayerfs/home/f002b6j/.local/lib/python2.7/site-packages/nipype/pipeline/engine.py", line 284, in connect
infostr))
Exception: Some connections were not found
Module inputnode has no output called eroded_wm

Module outputnode has no input called eroded_wm_registered

I'm using the latest commit and latest versions of FSL, FreeSurfer. I have the forked version of nipype.