pcamach2

@effigies, the fix of running `touch` on the `mri/aseg.auto_noCCseg.label_intensities.txt` file (https://github.com/Deep-MI/FastSurfer/issues/21#issuecomment-1103950005) resolves the error and allows sMRIPrep to complete. I added a short python function to my fork of smriprep/smriprep/utils/misc.py...

I removed the `fastsurfer_bool` variable and added the `check_fastsurfer` function to anatomical.py (https://github.com/pcamach2/smriprep/blob/pcamach2-fastsurfer-patch/smriprep/workflows/anatomical.py), which successfully builds the anat workflow and touches the label_intensities file. This runs as expected, so the...

@effigies, I am trying to connect the FastSurfer interface that I wrote and tested (https://github.com/pcamach2/smriprep/blob/pcamach2-fastsurfer-patch-dev/smriprep/interfaces/fastsurfer.py) into the overall sMRIPrep workflow. I added the following argument to the cli (https://github.com/pcamach2/smriprep/blob/pcamach2-fastsurfer-patch-dev/smriprep/cli/run.py) ```...

Hi Eduardo, I'm sure Matt will have better suggestions, but you may want to try the --low-mem option if the RAM is still an issue. Some issues that resemble memory...

@kurmukovai if the difference in voxel size between the CT and FLAIR is causing issues, you can try reslicing before transforming [https://dipy.org/documentation/1.2.0./examples_built/reslice_datasets/](https://dipy.org/documentation/1.2.0./examples_built/reslice_datasets/)

I feel comfortable closing this issue since it has been over a year and dipy has updated.

Hi @skoudoro, Totally understandable! Let me know if you want any help with the singularity and docker set up! Cheers, Paul

I think the C stands for component, coming from the barycentric coordinate system description of the diffusion tensor geometry ( see the definitions given near figure 4 in Jones 2002:...

@effigies, I must be missing something simple, but I have not been able to resolve this error in CircleCI testing: ``` #!/bin/bash -eo pipefail bash /tmp/src/smriprep/.circleci/ds005_run.sh --write-graph ^@^@Traceback (most recent...

No worries! Any help with the merge conflicts would be great, thanks!