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CHANGELOG.md

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CHANGELOG

  • 29/06/2022: rename some modules; improve argument parsing
  • 24/06/2022: specify subject/session flags once, add more long flagged arguments; add check for bash version
  • 21/06/2022: assigned some of the KWARGS-argument to long flagged arguments
  • 19/04/2022: remove default use of config file for fMRIprep; now specify it explicitly with the '-u' flag.
  • 20/12/2021: added '-u' flag for custom configurations file for fMRIprep
  • 29/10/2021: added '-x' flag for various options. Mainly to specify the session number for pRF-sessions, as you'd have to specify '-n prf' as session, but you'll probably like to specify a session number too. You can do that by specifying '-n prf -x 1'
  • 20/10/2021: specified input directory for URIS-MDD project for module 8 and 9. This project is not run through Pymp2rage, so needed adjustment. Set cat12-processing to 'brain' by default, as running spinoza_biassanlm before CAT12 (spinoza_brainextraction) is preferred. Assign 'spinoza_sinusfrommni' to module 7, rather than 'spinoza_averageanatomies', which is a pretty redundant module by now.
  • 18/10/2021: added the '-w' flag to specify Wagstyl's equivolumetric layering for layering mo- dule.
  • 18/08/2021: added the '-p' flag to specify the kind of model to use during pRF-fitting. 'Gauss' or 'norm'
  • 17/06/2021: added module 26, spinoza_profiling, to sample the values of a particular dataset across depth using call_nighresprofsamp to create profile of this dataset. Currently using this for URIS to create profiles of T1-values across depth
  • 06/04/2021: added '-l' and '-q' flags for master-command; with 'master -l ' you can look for a module number given a string. With 'master -m -q' you can ask to print the help-stuff from the specified modules
  • 15/03/2021: added '-t' flag for fMRIprep module to run either 'anat' or 'func' workflows
  • 10/02/2021: added subcortex parcellation module after 'layering' module. With that, i moved the spinoza_line2surface module to module 25
  • 21/01/2021: added session-switch to most modules to account for situations where one might have multiple sessions or even none. Default is set to '1', so if you want to pro- cess a different session, specify so with the '-n' flag when calling "master -m X"
  • 20/01/2021: added subject-switch to more modules: 'qmrimaps', 'registration', 'biascorrection', 'brainextraction', 'createduraskullmask', 'sagittalsinus', 'denoising', 'fitprfs', 'bestvertex', 'segmentfast' changed 'spinoza_estimateunit1' to 'spinoza_qmrimaps'
  • 14/01/2021: added subject-switches to 'masking', 'fmriprep', 'mgdm', 'region' modules, so that in addition to positional arguments a '-s' switch can be specified to loop only over the input subject, not the entire 'sub-' list. This '-s' flag HAS to be specified before the positional arguments!
  • 12/01/2021: added overwrite mode for the GDH-pipeline, in addition to nicer specification of paths in the FreeSurfer and Nighres modules (better path specification instead of 'just' DIR_DATA_HOME and DIR_DATA_DERIV)
  • 15/12/2020: added overwrite mode for certain modules (00 and 13)
  • 10/12/2020: added module to do recon after nifti-conversion (moved other modules down)
  • 25/10/2020: added module to do pRF-fitting with pRFpy (moved other modules down)
  • 24/10/2020: added module to do denoising with pybest (moved other modules down)
  • 21/10/2020: added module to project line to surface with registration cascade
  • 30/09/2020: added the module to determine the best vertex with pycortex as module 14
  • 23/09/2020: removed bias field correction for UNIT1 module, as we'll do that with fMRIprep leaving out freesurfer segmentation from the SEG-module. Included in fMRIprep