I run a variation of this script on my own data set:
When running the spm Level1Design I receive this error:
Traceback (most recent call last):
File “”, line 1, in
File “/home/or/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/core.py”, line 524, in run
outputs = self.aggregate_outputs(runtime)
File “/home/or/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/core.py”, line 625, in aggregate_outputs
File “/home/or/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/core.py”, line 618, in aggregate_outputs
setattr(outputs, key, val)
File “/home/or/anaconda3/lib/python3.6/site-packages/nipype/interfaces/base/traits_extension.py”, line 112, in validate
TraitError: The trait ‘spm_mat_file’ of a Level1DesignOutputSpec instance is an existing file name, but the path ‘/home/or/SPM.mat’ does not exist.
The path is correct of course but there is no SPM.mat file there.
What am I missing?
Does anyone else received such an error message before?
Any help will be appreciated.
I have the exact same error and have posted an issue on github: https://github.com/nipy/nipype/issues/2880
My guess is: as inputs to you level1design you have a mask_image and also a custom spm_mat_dir? If so, a temporary SPM.mat file is created in the initial working folder of MATLAB. If you change the spm_mat_dir input, it will not find this SPM.mat file anymore.
I created a workaround (in the thread at github) for the time being.
I’m not sure if we have the same issue or not.
I’m able to run if smoothly and only encounter problems when I try to add regressors to the info file (using Bunch). I take the regressors from fmriprep pipeline and I think there might be some issues around that.
@satra I don’t feel qualified to give advice on SPM interfaces, if you can give us a hint I can take it from there tomorrow.
I have solved the issue. And I think the error message is misleading.
The issue was associated with the fact the the Bunch object was array and not an array of lists (when I added the confounds).
After changing that it ran without a problem.
I think it might be a good idea to change the error message (something like - ‘unfit data’ or else).
Can you file a new issue on nipype’s repository (https://github.com/nipy/nipype/issues/new) requesting such change?