What’s new?

v0.1.2

Fixed

  • Added missing semicolon to SC line 74
  • Issue with transformations management in SC when only AFFINE was applied
  • ‘str_dwi_affine’ variable name corrected dwi in -SC
  • Typo in notification of completition (a missing ‘s’) in proc_struc
  • Variable changed from th to TH in qc_surf.py
  • Issue with the reo file when the original T1w was nii not nii.gz and single run

Enhaced

  • Reorder c69 surfaces, plot T1onDWI either Affine or SyN on micapipe_qc
  • Added version to group QC table in utilities.sh
  • Added full path to nifti_capture.py in proc_dwi
  • Created a conte69 dir with mkdir -p in freesurfer directory
  • When using antsApplyTransforms replace transformations in tissue_series with variable ($transformsInv)
  • Added option to apply only an affine registration in proc_dwi
  • Added conte69 surfaces to the freesurfer dir and pipeline
  • Increase compatibility if rpe and pe have different size in proc_dwi
  • Update function from app.add_stylesheet to app.add_css_file (conf.py)
  • Erase all MP-PCA and deGibbs files with micapipe_cleanup
  • Manages single session T1w.nii: compression to NIFTI_GZ
  • So not append invidivual QC log

Documentation

  • Updated python libraries in README
  • Added gradients tutorial single subject
  • Update native sphere visualization in R with fsbrain
  • Updated surfaces, updated FAQ and references
  • Surface visualization (python)
  • Update doi and reference of SUDMEX dataset
  • Added ipynb and R files, organized surfaces and gradients
  • Added tutorial ‘Matrices’, made draft of Surface visualization and Gradients

v0.1.1

  • Documentation update
  • Added a missing string in the output names of 02_proc-dwi.sh “space-dwi_from-dwi_to-nativepro_mode-image_desc-affine_
  • Added umask to micapipe_cleanup
  • Fix a typo in the mica-pipe help (distortion)
  • Rename flags and variables in micapipe_anonymize from refacePro to warpface
  • Update print version in mica-pipe
  • micapipe_qc: added print info for Sankey diagram and Surfaces visualization
  • micapipe_qc: added full path to nifti_capture.py
  • Fixed an error in 02_proc-rsfmri.sh, wrong assignation of fmri_pe!

v0.1.0 (Roadrunner)

  • We are currently on the initial release version of the micapipe
  • From now on, we’ll keep track of the major changes here
  • Start keeping changelog 👾🤓👾