Skull still visible in preproc_bold image and incorrect dimensions

[effigies]

Hi @rosaleen, thanks for the question.

The desc-preproc_bold.nii.gz files are not skull-stripped, but we provide a mask desc-brain_mask.nii.gz files that are in the same space. This is generally useful for assessing the quality of the mask. Because many tools allow you to load a BOLD series and a mask simultaneously, it seemed wasteful to output a second time series with the mask applied. However, if you need it, you can get a skull-stripped time series with fslmaths:

fslmaths sub-11_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz \
   -mas sub-11_task-rest_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz \
   out_file.nii.gz

@rosaleen

Ideally, I’d like them to be either 91x109x91 with a voxel size of 2x2x2 or 60x71x60 with a voxel size of 3x3x3. Would a different template work? I’m just using the default at the moment.

You should be able to do this with --output-spaces MNI152NLin2009cAsym_desc:res-2. You can add other spaces, as well, if desired. See the Workflow configuration and the Spaces documentation.