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Workflows and interfaces for neuroimaging packages
The function `_list_outputs` in `DWIBiasCorrect` doesn't take into account the fact that `output_file` is not a mandatory input, thus making any pipeline using this interface without specifying the output crash....
## Summary The underlying issue shows clearly with `3.10`, which is interpreted as `3.1`. This does not fix anything that wouldn't currently work. However, for documentation purposes, I feel it...
This PR adds explicit [permissions section](https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#permissions) to workflows. This is a security best practice because by default workflows run with [extended set of permissions](https://docs.github.com/en/actions/security-guides/automatic-token-authentication#permissions-for-the-github_token) (except from `on: pull_request` [from external...
When I'm trying to normalize some data using spm.Normalize12() with the following code, everything goes fine ``` norm = spm.Normalize12() norm.inputs.image_to_align = os.path.join(T1_output_folder,'T1.nii') norm.inputs.apply_to_files = [os.path.join(Recon_output_folder,'rrrRecon_full_run1.nii'),os.path.join(Recon_output_folder,'rrrRecon_full_run2.nii')] norm.run() ``` But when...
@satra Do we care about publishing Docker images? I believe they were mainly used for courses, which I assume are no longer going to be using nipype 1?
The main figure is now small. Main other change is upgrading Sphinx 4.5 to 5.0. Investigation and PRs welcome! ### 1.8.2 https://nipype.readthedocs.io/en/1.8.2/  ### 1.8.1 https://nipype.readthedocs.io/en/1.8.1/ 
## Summary This PR updates the PETsurfer interface in nipype to be in line with the FreeSurfer implementation and closes issue https://github.com/nipy/nipype/issues/3601. ## List of changes proposed in this PR...
- added Hybrid Surface and Volume Segmentation ('hsvs') option to the 5TT image generation class - removed the in_file existing requirement (exists=True -> exists=False) for 5ttgen because hsvs requires a...
This PR updates the mrtrix3 interface in nipype and closes issue #3612 List of proposed changes: 1. Added "MaskFilter" for dilate/erode filteres 2. Added "MTnormalise" 3. Added "Generate5tt2gmwmi"
### Summary I'm running a Bayesian analysis using [Per Síden's code](https://github.com/psiden/BFAST3D) using spatial priors and the resulting SPM.mat files are massive for ultra high field data (upwards of 2 GB)....
