[BUG]: ImportError: cannot import name 'NUMPY_MMAP' from 'nipype.utils'

[FL33TW00D]

Hi there,
I am using QSIPrep v0.11.0 through the singularity container using the following command:

singularity run --cleanenv --bind /gpfs/home/vhe17qgu/qsiprep:/qsiprep qsiprep-0.11.0.sif \ qsiprep_test_data \ output_dir \ participant \ --work-dir working_dir \ --fs-license-file license.txt \ --nthreads 8 --unringing-method mrdegibbs \ --hmc-model 3dSHORE \ --prefer-dedicated-fmaps \ --output-resolution 1

I am receiving the following error:
ImportError: cannot import name 'NUMPY_MMAP' from 'nipype.utils'

It seems like this is due to an outdated import according to the Nipype repo? It's a brand new image so not sure why this would happen since the issue was resolved in May 2017 at the following ticket: #1898

EDIT:
I pulled the QSIPrep repo and looked through the code, just looks like a change from

from nipype.utils import NUMPY_MMAP -> from nipype.utils.config import NUMPY_MMAP

will do the job. unfortunately I am unaware of how to edit the code and then rebuild it into a Singularity Container.

Please let me know your thoughts.

Many Thanks,
Chris

[fredrmag]

I think this is due to nipype 1.5.0 has taken away the NUMPY_MMAP altogether: nipy/nipype#3121

[FL33TW00D]

I think this is due to nipype 1.5.0 has taken away the NUMPY_MMAP altogether: nipy/nipype#3121

Ah that does seem to be the case.
I am unsure of the solution here then, waiting for @mattcieslak to hopefully guide me.

Thanks for the reply.

[fredrmag]

I believe that the solution to this, is to:

1. remove all from nipype.utils import NUMPY_MMAP lines in the code.
2. change all nb.load commands from nii = nb.load(volume, mmap=NUMPY_MMAP) to nii = nb.load(volume)

[fredrmag]

Seems to only be in one file:
https://github.com/PennBBL/qsiprep/blob/e1f7db9ff4a393fdd0748f52451e91d20008ccb5/qsiprep/workflows/fieldmap/utils.py#L53-L66

[fredrmag]

I have opened a PR (#175) to try to fix it.

[FL33TW00D]

@fredrmag Thank you so much for fixing this.