Group ICA Errors

[thomas.nickson]

Hi All,

I keep getting this weird error when doing group ICA. It just says:

nipype.utils.filemanip.FileNotFoundError: File/Directory '/sdata/images/people/tnickson/wyeth/NipypeFiles/connections/groupA/report' not found for MELODIC output 'report_dir'.

but shouldn't that part of the script be creating that folder?


Running: melodic -i /sdata/images/people/tnickson/wyeth/NipypeFiles/connections/_subjects_WD2_001/noiseFilter/mapflow/_noiseFilter0/Merged_S14568_Resting__dtype_mcf_mask_smooth_mask_gms_tempfilt_warp_maths_regfilt.nii.gz /sdata/images/people/tnickson/wyeth/NipypeFiles/connections/_subjects_WD2_002/noiseFilter/mapflow/_noiseFilter0/Merged_S14610_Resting__dtype_mcf_mask_smooth_mask_gms_tempfilt_warp_maths_regfilt.nii.gz --Oall -o /sdata/images/people/tnickson/wyeth/NipypeFiles/connections/groupA --report --tr=2.500000
Traceback (most recent call last):
  File "fslWyethICA.py", line 368, in <module>
    connections.run()
  File "/usr/lib/python2.6/site-packages/nipype/pipeline/engine.py", line 689, in run
    runner.run(execgraph, updatehash=updatehash, config=self.config)
  File "/usr/lib/python2.6/site-packages/nipype/pipeline/plugins/linear.py", line 38, in run
    node.run(updatehash=updatehash)
  File "/usr/lib/python2.6/site-packages/nipype/pipeline/engine.py", line 1386, in run
    self._run_interface()
  File "/usr/lib/python2.6/site-packages/nipype/pipeline/engine.py", line 1496, in _run_interface
    self._result = self._run_command(execute)
  File "/usr/lib/python2.6/site-packages/nipype/pipeline/engine.py", line 1622, in _run_command
    result = self._interface.run()
  File "/usr/lib/python2.6/site-packages/nipype/interfaces/base.py", line 947, in run
    outputs = self.aggregate_outputs(runtime)
  File "/usr/lib/python2.6/site-packages/nipype/interfaces/base.py", line 1041, in aggregate_outputs
    raise FileNotFoundError(msg)
nipype.utils.filemanip.FileNotFoundError: File/Directory '/sdata/images/people/tnickson/wyeth/NipypeFiles/connections/groupA/report' not found for MELODIC output 'report_dir'.
Interface MELODIC failed to run. Inputs:
ICs = <undefined>
approach = <undefined>
args = <undefined>
bg_image = <undefined>
bg_threshold = <undefined>
cov_weight = <undefined>
dim = <undefined>
dim_est = <undefined>
environ = {'FSLOUTPUTTYPE': 'NIFTI_GZ'}
epsilon = <undefined>
epsilonS = <undefined>
ignore_exception = False
in_files = ['/sdata/images/people/tnickson/wyeth/NipypeFiles/connections/_subjects_WD2_001/noiseFilter/mapflow/_noiseFilter0/Merged_S14568_Resting__dtype_mcf_mask_smooth_mask_gms_tempfilt_warp_maths_regfilt.nii.gz', '/sdata/images/people/tnickson/wyeth/NipypeFiles/connections/_subjects_WD2_002/noiseFilter/mapflow/_noiseFilter0/Merged_S14610_Resting__dtype_mcf_mask_smooth_mask_gms_tempfilt_warp_maths_regfilt.nii.gz']
log_power = <undefined>
mask = <undefined>
max_restart = <undefined>
maxit = <undefined>
mix = <undefined>
mm_thresh = <undefined>
no_bet = <undefined>
no_mask = <undefined>
no_mm = <undefined>
non_linearity = <undefined>
num_ICs = <undefined>
out_all = True
out_dir = <undefined>
out_mean = <undefined>
out_orig = <undefined>
out_pca = <undefined>
out_stats = <undefined>
out_unmix = <undefined>
out_white = <undefined>
output_type = NIFTI_GZ
pbsc = <undefined>
rem_cmp = <undefined>
remove_deriv = <undefined>
report = True
report_maps = <undefined>
s_con = <undefined>
s_des = <undefined>
sep_vn = <undefined>
sep_whiten = <undefined>
smode = <undefined>
t_con = <undefined>
t_des = <undefined>
terminal_output = stream
tr_sec = 2.5
update_mask = <undefined>
var_norm = <undefined>

Thanks,

Tom

[thomas.nickson]

Hi All,

I thought that I would alert you to that fact that after some hunting this is a bug.

The problem is that the output of Nipype's melodic command is malformed and as such does not run properly in group mode. Nipype lists the subjects like this, "subject1 subject2 subject3" whereas this is the required output "subject1,subject2,subject3". No spaces! Otherwise for some reason it will dump the output in to the first folder it sees and Nipype will complain that no appropriate folders were created.

I will file a bug report on this and hopefully I can submit a fix. Any hints as to what I would need to change. I feel like this should be an easy one but I don't know where to look. Any help appreciated,

thanks,

Tom

[Satrajit Ghosh]

hi tom,

could you please point out where nipype does this?

this is the cmdline generated by MELODIC interface on the example in the doctest. is the in_file option where you were thinking about the spaces or is it somewhere else?

'melodic -i functional.nii,functional2.nii,functional3.nii -a tica --bgthreshold=10.000000 --mmthresh=0.500000 --nobet -o groupICA.out --Ostats --Scon=subjectDesign.con --Sdes=subjectDesign.mat --Tcon=timeDesign.con --Tdes=timeDesign.mat --tr=1.500000'

cheers,

satra

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