MPM / QSM processing

This package preprocesses EPI based MPM/QSM data, performs an hMRI based MPM analysis and prepares the QSM analysis (not included, ask Monica for information)

Installation

To install the MPMQSM_preproc use either

• python setup.py develop
• python setup.py install

BIDS data structure

This package uses the BIDS data format. Data has to be organized before in the following manner:

MT.mat PD.mat cest fmap DZNE_subj-02_ses-01_fmap-b1-con.json DZNE_subj-02_ses-01_fmap-b1-con.nii DZNE_subj-02_ses-01_fmap-b1.json DZNE_subj-02_ses-01_fmap-b1.nii magn mpm DZNE_subj-02_ses-01_MTw_e1.json DZNE_subj-02_ses-01_MTw_e1.nii DZNE_subj-02_ses-01_MTw_e1_ph.json DZNE_subj-02_ses-01_MTw_e1_ph.nii DZNE_subj-02_ses-01_MTw_e2.json DZNE_subj-02_ses-01_MTw_e2.nii DZNE_subj-02_ses-01_MTw_e2_ph.json DZNE_subj-02_ses-01_MTw_e2_ph.nii DZNE_subj-02_ses-01_MTw_e3.json DZNE_subj-02_ses-01_MTw_e3.nii DZNE_subj-02_ses-01_MTw_e3_ph.json DZNE_subj-02_ses-01_MTw_e3_ph.nii DZNE_subj-02_ses-01_MTw_e4.json DZNE_subj-02_ses-01_MTw_e4.nii DZNE_subj-02_ses-01_MTw_e4_ph.json DZNE_subj-02_ses-01_MTw_e4_ph.nii DZNE_subj-02_ses-01_PD_e1.json DZNE_subj-02_ses-01_PD_e1.nii DZNE_subj-02_ses-01_PD_e1_ph.json DZNE_subj-02_ses-01_PD_e1_ph.nii DZNE_subj-02_ses-01_PD_e2.json DZNE_subj-02_ses-01_PD_e2.nii DZNE_subj-02_ses-01_PD_e2_ph.json DZNE_subj-02_ses-01_PD_e2_ph.nii DZNE_subj-02_ses-01_PD_e3.json DZNE_subj-02_ses-01_PD_e3.nii DZNE_subj-02_ses-01_PD_e3_ph.json DZNE_subj-02_ses-01_PD_e3_ph.nii DZNE_subj-02_ses-01_PD_e4.json DZNE_subj-02_ses-01_PD_e4.nii DZNE_subj-02_ses-01_PD_e4_ph.json DZNE_subj-02_ses-01_PD_e4_ph.nii DZNE_subj-02_ses-01_T1_e1.json DZNE_subj-02_ses-01_T1_e1.nii DZNE_subj-02_ses-01_T1_e1_ph.json DZNE_subj-02_ses-01_T1_e1_ph.nii DZNE_subj-02_ses-01_T1_e2.json DZNE_subj-02_ses-01_T1_e2.nii DZNE_subj-02_ses-01_T1_e2_ph.json DZNE_subj-02_ses-01_T1_e2_ph.nii DZNE_subj-02_ses-01_T1_e3.json DZNE_subj-02_ses-01_T1_e3.nii DZNE_subj-02_ses-01_T1_e3_ph.json DZNE_subj-02_ses-01_T1_e3_ph.nii DZNE_subj-02_ses-01_T1_e4.json DZNE_subj-02_ses-01_T1_e4.nii DZNE_subj-02_ses-01_T1_e4_ph.json DZNE_subj-02_ses-01_T1_e4_ph.nii pulses

this includes - fmap-b1 relative flipangle map of the ptx pulse (or CP, if no ptx is measured) - fmap-b1-con maximal contrast from the $B1$ maps (used for SPM registration) - mpm/ $T1$, MT and PD weighted, multi echo data

Usage

usage: mpmqsm_preproc [-h] --path PATH [--den DEN] --site SITE --sub SUB --ses SES [--ptx]

--path PATH path to MPM/QSM data, folder, where the BIDS structure originates (default: None) --den DEN boolean, shall the raw data be denoised? default = true (default: True) --site SITE exact name of site (eg DZNE) (default: None) --sub SUB exact name of subject (eg subj-01) (default: None) --ses SES exact name of session (eg ses-01) (default: None) --ptx create log file? default true (default: True)

Output

MPM output can be found in

derivates/SITE/SUBJECT/SESSION/mpm/maps/Results

QSM input (for Monica's analysis)

derivates/SITE/SUBJECT/SESSION/qsm/ROCombine