Matt Cieslak

this is good to know, I am in QC mode right now and will be adding them

Hi @m-petersen did you ever figure this out?

can you try singularity with `--containall`? It looks like a python library in your home directory is being loaded into the container (`/home/arovai/.local/lib/python3.8/site-packages/nipype/interfaces/base/core.py`)

Note: Check in with nipreps/dmriprep#24

Thank you @hfxcarl this is correct in most cases. If your original T1w had an oblique acquisition then the obliquity is removed before any processing happens (this avoids a bug...

Do you still have the working directory from when you ran qsiprep? The T1w is transformed to T1wACPC space through a rigid transform. It is a soon-to-be-fixed bug that the...

Hi @araikes, happy to see qsiprep and cubids being used together! In cases like this, where there are a ton of differences between an acquisition and the dominant group, we'd...

I have no problem forcing the mask to be of type int. This wouldn't cause a problem for any of the other recon workflows and is a sensible default. Would...

You can use c3d to convert between ITK transforms and FSL-style transforms. Something like `c3d_affine_tool -ref sub-130917_desc-preproc_T1w.nii.gz -src your_non-acpc_image.nii -itk sub-130917_from-T1wNative_to-T1wACPC_mode-image_xfm.mat -ras2fsl -o fsl_transformation_file.mat` should work. More robust would be...

@julfou81 and @dyhan316 are your original T1w images oblique?