v0.2.3

micapipe v0.2.3

• 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.

1. -SWM: superficial white matter generation and mapping in nativepro space.
2. -SWM_MPC: Superficial white matter MPC in native qMRI space.

v0.2.2

micapipe v0.2.2 'Northern Flicker'

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

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

v0.2.1

• 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

micapipe v0.2.0 'Northern Flicker'

👥 Compatible with multiple acquisitions (func, dwi, MPC). multiple quantitative maps, DWI acquisitions and func acquisitions including task
🧠 We improved the registration between between modalities to optimize the performance.
🌐 Surface mapping from native space in all modules.
🔬 Optimize to process ultra high resolution 7T datasets, with new CNN based processing tools. (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.
✨ Connectomes are NOW stored as GIFTI instead of txt. these files use less storage and are faster to load.
⚡️ 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, registration)

v0.1.5

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

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.