What’s new?

v0.2.+ ‘Northern Flicker’

  • All versions 0.2.0 and above are compatible with each other and have the same software versions.

  • Each version update has code improvement and enhancements based on the comments of the users.

  • We highly recommend to use the latest version.

v0.2.3, Jan 18, 2024


  • Updated RtD

  • Added tSNR volumetric and mapping, matched names on all scripts, and updated QC_subj accordingly

  • Center-aligned images before affine registration.

  • Rename transformation json before it was being overwritten by multiple func acquisitions (e.g. task)

  • Quiet percentage of completition of MRtrix

  • Center align b0 and T1 for the first affine registration

  • New flag -upsample_dwi for proc_dwi

  • Fixed MPC cleanup

  • Upgraded flair preprocessing with WM-peak, GM mode normalization

  • Fixed SINGLE session issues (e.g proc_func and QC)

  • Fixed R libraries issues for fls-fix in new Dockerfile

New Modules

  • Both modules include: json files, subject QC and cleanup integration.

  • SWM: superficial white matter generation and mapping in nativepro space.

  • SWM_MPC: Superficial white matter MPC in native qMRI space.

v0.2.2, Aug 9, 2023


  • FIX issue with multiple acquisitions when -proc_dwi was used with -dwi_acq. Including the following modules SC, QC and QC_subj.

  • FIX instance when multi echo processing has no spike regression file now calculates the nuisance regression correctly.

  • FIX an issue with the dimensions of the tSNR file in proc_func.

QC group

  • Set higher thresholds for GD and SC in the similarity subjects matrices for better outlier detection.

  • NEW vertex-wise and ROI variance per feature.

  • NEW histograms of features and variances per ROI and vertex-wise.


  • NEW a surface plot of the tSNR to the proc_func module in QC_subj.

v0.2.1, Jun 26, 2023

  • We fixed the usage of -QC and -QC_subj for those datasets with single session.

  • Update a conditional in proc_surf that search for the ribbon.mgz

  • Add a missing variable in -SC when using -autotrack

v0.2.0 ‘Northern Flicker’, Jun 16, 2023

  • 👥 Compatible with multiple acquisitions (func, dwi, MPC). multiple quantitative maps, DWI acquisitions and func acquisitions including task

  • 🧠 Improved registrations between modalities. We improved the registration between multiple acquisitions to optimize the performance.

  • 🌐 Surface mapping from native space in all modules.

  • 🔬 Optimized for high resolution processing (tested on 0.5-1mm3, e.g 7T)

  • 💦 MP2RAGE processing workflow (3T and 7T) for structural images, including a cleaning of the salt and pepper background noise.

  • ✨ Optimize to process ultra high resolution 7T datasets, with new CNN based processing tools.

  • ⚡️ NEW FLAIR processing module

  • 🔍 New QC subject and group level more informative with a lot of new features and pdf (new json files for QC)

  • 👾 New algorithms (brain mask, surface reconstructions - fastsurfer)

  • 🛥️ Docker container

  • 🐛 A lot of bugs fixed

v0.1.5, Jun 10, 2023

General changes

  • Update print help

  • Removed unused flags

  • Update the documentation (partially)

  • UPDATE jsons to increase pyBIDS compatibility

  • FIX bug on MPC output directory

`proc_func` and `FC`

  • Rename flags on proc_func -regress_WM_CSF to -NSR

  • FIX bug on glm regression matrix of cofounding (higher precision)

`proc_dwi` and `SC` upgrade

  • Manage multiple acquisitions -dwi_acq

  • micapipe_cleanup is up to date to erase multiple acquisitions

  • -b0thr allows the user to set a threshold to determine the volumes that correspond to b=0, default=61

  • -no_bvalue_scaling disable the diffusion b-values scaling of the corresponding DWI norm (see Mrtrix3 for further info)

v0.1.4 ‘Roadrunner’, Nov 3, 2022

  • Update FSL from 6.0.0 to 6.0.3

  • mica-pipe command goes to micapipe

  • To print help should specify it with the flag micapipe -h or micapipe -help

  • post_structural will always run schefer-400 by default if is not included in the -atlas list

  • proc_rsfmri is deprecated and replaced by proc_func

  • proc_func handles more than one functional acquisition (e.g. tasks), as well as multi echo data (tedana https://github.com/ME-ICA/tedana).

  • proc_func Added option to drop the first 5 TRs -dropTR (by default is not dropped)

  • proc_func Added option to not run the functional connectomes -noFC (only func surface data)

  • proc_func Added 6 parameters of motion to the regression of -regress_WM_CSF (func~spikes+6motion+wm+csf)

  • proc_func Added 6 parameters of motion to the regression of -GSR (func~spikes+6motion+wm+csf+gs)

  • MPC can processes more than one quantitative map (at a time) with the flag -mpc_acq <qMRI_name>

  • micapipe_cleanup can be called from micapipe command: micapipe -cleanup

  • micapipe -cleanup uses the string -acqStr to erase multiple acquisitions of -proc_func and -MPC

  • Improved comments and print logs of -proc_func and FC.py

  • proc_func generates new jsons files of each acquisition with metadata about processing and completion status

  • proc_func exit status when Melodic/FIX fail

  • -QC_subj is not compatible with proc_func yet…. or with MPC multiple acquisitions but it is still with the old proc_rsfmri outputs

  • NOTE: the read the docs is not updated yet.



  • 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


  • 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


  • 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


  • 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 ‘Wobbly’

  • 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 👾🤓👾