[Nipype] Wrong naming of output files in mcflirt

aryan-bampal · January 2, 2021, 10:45am

Hi everyone,
i’m running nipype and getting this error from mcflirt interface during the preprocessing phase:-
#################################################
Traceback (most recent call last):
File “/home/USER/data/nipype/nipype/pipeline/plugins/multiproc.py”, line 67, in run_node
result[“result”] = node.run(updatehash=updatehash)
File “/home/USER/data/nipype/nipype/pipeline/engine/nodes.py”, line 516, in run
result = self._run_interface(execute=True)
File “/home/USER/data/nipype/nipype/pipeline/engine/nodes.py”, line 635, in _run_interface
return self._run_command(execute)
File “/home/USER/data/nipype/nipype/pipeline/engine/nodes.py”, line 741, in _run_command
result = self._interface.run(cwd=outdir)
File “/home/USER/data/nipype/nipype/interfaces/base/core.py”, line 436, in run
outputs = self.aggregate_outputs(runtime)
File “/home/USER/data/nipype/nipype/interfaces/base/core.py”, line 544, in aggregate_outputs
raise FileNotFoundError(msg)
FileNotFoundError: No such file or directory ‘/home/USER/data/ds000114/output/workingdir/preproc/_subject_id_01_task_name_fingerfootlips/mcflirt/sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_mean_reg.nii’ for output ‘mean_img’ of a MCFLIRT interface
#################################################
so the software is searching for this file:-
“sub-01_ses-test_task-fingerfootlips_bold_roi_mcf_mean_reg.nii”
in the output folder
But i’m getting this file instead :-
"sub-01_ses-test_task-fingerfootlips_bold_roi_mcf.nii_mean_reg.nii "
this file has an extra extension (.nii) attached to it and hence this file is not picked up by the software

Any ideas would be much appreciated?

Thank you,

Cherkas · January 4, 2021, 2:20am

Hi aryan-bampal, do you use any substitutions to change output file names? If so - remove them or connect properly to your folder (datasink) so the pipeline can pick them up.

aryan-bampal · February 16, 2021, 7:08pm

Hi Cherkas ,
Removing the the substitution results in the same error .

aryan-bampal · March 2, 2021, 7:52am

Hi Cherkas ,
There seems to be some problem in using fsl software . So i have used AFNI software to preprocess the NIFTI dataset such as :- despiking , motion correction, slice correction , detrending , smoothing . The output of these libraries is always BRIK so i repeatedly convert BRIK to NIFTI becoz the input file to these software is NIFTI .
My problem is :- after doing despiking , motion correction, slice correction
Im getting the image as:-

After detrending , i get the image as :-

There is significant signal change between the voxel of the same image .
There is supposed to be little changes as detrending removes hardware artifacts .
Is there any error in what i am doing ??