Nipype workflow wanted to find the file of nested folder

nipype
selectfiles

#1

Attached is the result of crashfiles;

File: /media/nufas/ba32d503-d5ae-47f8-94a6-5318a1ce1fdf/home/farahana/Documents/dataset/crash-20180308-203349-nufas-selectfiles.a0-fcdd7b0c-9a49-4d9c-9638-9223ed367e8a.pklz
Node: antsflow.selectfiles
Working directory: /media/nufas/ba32d503-d5ae-47f8-94a6-5318a1ce1fdf/home/farahana/Documents/dataset/ds109_raw/output/workingdir/antsflow/_fwhm_id_4_subject_id_sub005/selectfiles


Node inputs:

base_directory = ds109_raw/output/
force_lists = False
fwhm_id = 4
ignore_exception = False
raise_on_empty = True
sort_filelist = True
subject_id = sub005



Traceback: 
Traceback (most recent call last):
  File "/home/nufas/anaconda3/lib/python3.6/site-packages/nipype/pipeline/plugins/linear.py", line 44, in run
    node.run(updatehash=updatehash)
  File "/home/nufas/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 487, in run
    result = self._run_interface(execute=True)
  File "/home/nufas/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 571, in _run_interface
    return self._run_command(execute)
  File "/home/nufas/anaconda3/lib/python3.6/site-packages/nipype/pipeline/engine/nodes.py", line 650, in _run_command
    result = self._interface.run(cwd=outdir)
  File "/home/nufas/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 517, in run
    outputs = self.aggregate_outputs(runtime)
  File "/home/nufas/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/core.py", line 591, in aggregate_outputs
    predicted_outputs = self._list_outputs()
  File "/home/nufas/anaconda3/lib/python3.6/site-packages/nipype/interfaces/io.py", line 1406, in _list_outputs
    raise IOError(msg)
OSError: No files were found matching con template: /media/nufas/ba32d503-d5ae-47f8-94a6-5318a1ce1fdf/home/farahana/Documents/dataset/ds109_raw/output/workingdir/antsflow/_fwhm_id_4_subject_id_sub005/selectfiles/ds109_raw/output/datasink/1stLevel/sub005/fwhm-4/???_00??.nii

#2

Can you please share the code you are trying to run.

What is the structure of the data folder? what is inside /media/nufas/ba32d503-d5ae-47f8-94a6-5318a1ce1fdf/home/farahana/Documents/dataset/ds109_raw/output/workingdir/antsflow/_fwhm_id_4_subject_id_sub005/selectfiles/ds109_raw/output/datasink/1stLevel/sub005/fwhm-4 directory?


#3

I am trying to run this:
graph

The simple normalization from here but with different dataset.

I don’t have that folder. it is nested inside experiment_dir.


#4

The error you have “OSError: No files were found matching con template”, so it looks like you’re trying to select a file that is not on your machine. It’s hard for me to say what is wrong without seeing your code (with your specific changes) and knowing where are the files that you are hopping to select.

The notebook example_normalize.ipynb was written to work with a specific dataset (/data/ds000114) and after running example_preprocessing.ipynb and example_1stlevel.ipynb, since it uses output of the 1stLevel as input to the workflow. If you want to use it with your own data, you have to carefully change all directories (e.g. experiment_dir) and templates used in SelectFiles to match your directories and files you want to use.
It might be useful to experiment with the original dataset first to see how SelectFIles work etc. More on SelectFiles you can also find in this notebook.