Audrey Houghton

Feature Request: Writing Inside the Model Path

1

We noticed that nnUNet_predict writes inside the trained model directory. This causes a problem for when someone is trying to run this inside a container. This is specifically where it...

allow CuBIDS to concatenate subjects together from separate directories to be able to run with data on the S3

6

Use case example: pull subject directory into a temp directory run cubids-validate, cubids-group on that subject, do this with all subjects in an S3 bucket, and concatenate them into one...

Choose Head Size Based off of age of Participant

3

### A short summary of what you would like to see in *NiBabies*. Scale brain size flag based off of the age of the participant. Will need to find or...

Fails for anat only data when --ignore func flag isn't specified

2

If you have data that contains some subjects with functional data and some without, you cannot submit one run command for the pipeline. You have submit one command for the...

``` def get_readoutdir(metadata): """ get readout direction from bids metadata. !!Note that this method only applies where the nifti orientation is RAS!! :param metadata: grabbids metadata dict. :return: unwarp dir...

I am able to process data that doesn't have fieldmaps if no DWI data is present. If DWI data is present and there are no fieldmaps, it fails looking for...