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.

General

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

General

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.

QC_subj

👥 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

General changes

`proc_func` and `FC`

`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)

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.

Fixed

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

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!