a repository for small (neuroinformatic related) code snippets that might safe you time and ease up your coding life
We all know this: on every other occasion we need to do something with our data for which we don't have a script that does this certain job automatically, because we either need it only rarely or the commands are easily pipe together (e.g. checking the outputs of a certain function, reorienting some images, etc.). But some of those functions and applications occur very repeatedly and persistent, creating the feeling of being Bill Murray in a neuroinformatics version of Groundhog Day. Not that we don't like groundhogs, we just thought that the scripts we're using regarding this manner might also be helpful for others:
| script | function | prerequisites |
|---|---|---|
| BIDS_fslreorient_pydeface.sh | apply fslreorient2std, followed by pydeface to every structural image in a BIDS formatted data set | data set in BIDS format, python2.something, fsl, pydeface, nipype, nibabel |
| check_freesurfer_output.sh | visualize some important outputs of FreeSurfer's recon-all for a brief check | FreeSurfer |
| disc_vol.py | discard certain amount of volumes from the beginning of a given fMRI run | data set in BIDS format, python3.something, nibabel |