2. Single Subject Templates

All images that passed quality assessment, and had a corresponding image from another session for the same subject, were used to construct single subject templates (pennbbl/antssst:0.0.7, https://github.com/PennBBL/antssst/wiki). In order to ensure that all images were oriented correctly (RAS), the pre-processed t1-weighted images from fMRIPrep were used as input (i.e., sub-*_ses-*_desc-preproc_T1w.nii.gz). All images were N4-bias field corrected, but were not skull-stripped, as the extra features are useful for registration purposes. Details for the structural pre-processing stream in fMRIPrep can be found here. Note, all images were processed independently (i.e., the longitudinal stream was not utilized).

pennbbl/antssst:0.0.7 utilizes the following arguments for antsMultivariateTemplateConstruction.sh (modified to use a CC radius of 3 instead of 5):

1. -d 3 indicates that the images to be registered to one another are three dimensional
2. -o indicates the output directory
3. -n 0 indicates not to perform N4 bias field correction, as this has already been applied to the T1w images
4. -m 40x60x30 indicates the maximum number of iterations in each registration in the x, y and z directions
5. -i 5 indicates the number of times a given image is registered to the template
6. -c 0 indicates not to utilize parallel computation
7. -z specifies the reference image, such that all images other than this one will be rigidly aligned to it as a first pass at creating the single subject template