mp2rage: Compute a T1 map using MP2RAGE¶
- 1. Print mp2rage information
- 2. Setting model parameters
- 2.a. Create mp2rage object
- 2.b. Set protocol and options
- 2.b.1 Set protocol the CLI way
- 2.b.2 Set protocol and options the GUI way
- 3. Fit MRI data
- 3.a. Load input data
- 3.b. Execute fitting process
- 3.c. Display FitResults
- 3.d. Save fit results
- 3.e. Re-use or share fit configuration files
- 4. Simulations
- 4.a. Single Voxel Curve
- 4.b. Sensitivity Analysis
- 5. Notes
- 5.a. Notes specific to mp2rage
- 5.a.1 BIDS
- 5.a.2 Note-1
- 5.b. Generic notes
- 5.b.1. Batch friendly option and protocol conventions
- 5.b.2 Parallelization:
- 6. Citations
% This m-file has been automatically generated using qMRgenBatch(mp2rage) % for publishing documentation. % Command Line Interface (CLI) is well-suited for automatization % purposes and Octave. % % Please execute this m-file section by section to get familiar with batch % processing for mp2rage on CLI. % % Demo files are downloaded into mp2rage_data folder. % % Written by: Agah Karakuzu, 2017 % ==============================================================================
1. Print mp2rage information
mp2rage: Compute a T1 map using MP2RAGE Assumptions: N/A Inputs: (MP2RAGE) MP2RAGE UNI image. (B1map) Normalized transmit excitation field map (B1+). B1+ is defined as a normalized multiplicative factor such that: FA_actual = B1+ * FA_nominal. (OPTIONAL). (Mask) Binary mask to a desired region (OPTIONAL). (INV1mag) Magnitude image from the first GRE readout (OPTIONAL). (INV1phase) Phase image from the first GRE readout (OPTIONAL). (INV2mag) Magnitude image from the second GRE readout (OPTIONAL). (INV2phase) Phase image from the second GRE readout (OPTIONAL). Outputs: T1 Longitudinal relaxation time [s]. Corrected for B1+ bias IF the B1map is provided. R1 Longitudinal relaxation rate [1/s]. Corrected for B1+ bias IF the B1map is provided. MP2RAGE Combined MP2RAGE image if INV1mag, INV1phase, INV2mag, INV2phase images were provided but MP2RAGE was not. MP2RAGEcor MP2RAGE image corrected for B1+ bias if B1map is provided. Options: Inversion efficiency Efficiency of the inversion pulse (fraction). Authors: Agah Karakuzu, Mathieu Boudreau 2019 References: Please cite the following if you use this module: Marques, José P., et al. "MP2RAGE, a self bias-field corrected sequence for improved segmentation and T1-mapping at high field." Neuroimage 49.2 (2010): 1271-1281. In addition to citing the package: Karakuzu A., Boudreau M., Duval T.,Boshkovski T., Leppert I.R., Cabana J.F., Gagnon I., Beliveau P., Pike G.B., Cohen-Adad J., Stikov N. (2020), qMRLab: Quantitative MRI analysis, under one umbrella doi: 10.21105/joss.02343 Reference page in Doc Center doc mp2rage
2. Setting model parameters
2.a. Create mp2rage object
Model = mp2rage;
2.b. Set protocol and options
Protocol: MRI acquisition parameters that are accounted for by the respective model.
For example: TE, TR, FA FieldStrength. The assigned protocol values are subjected to a sanity check to ensure that they are in agreement with the data attributes.
Options: Fitting preferences that are left at user's discretion.
For example: linear fit, exponential fit, drop first echo.
2.b.1 Set protocol the CLI way
If you are using Octave, or would like to serialize your operations any without GUI involvement, you can assign protocol directly in CLI:
B0 = 7; Model.Prot.Hardware.Mat = [ B0 ];
Inv = 6; Exc = 0.0067; Model.Prot.RepetitionTimes.Mat = [ Inv Exc ];
InversionTimes = [0.8000; 2.7000]; % InversionTimes (s) is a vector of [2X1] Model.Prot.Timing.Mat = [ InversionTimes ];
FlipAngles = [4.0000; 5.0000]; % FlipAngles is a vector of [2X1] Model.Prot.Sequence.Mat = [ FlipAngles];
Pre = 35; Post = 72; Model.Prot.NumberOfShots.Mat = [ Pre Post];
See the generic notes section below for further information.
2.b.2 Set protocol and options the GUI way
The following command opens a panel to set protocol and options (if GUI is available to the user):
Model = Custom_OptionsGUI(Model);
If available, you need to close this panel for the remaining of the script to proceed.
Using this panel, you can save qMRLab protocol files that can be used in both interfaces. See the generic notes section below for details.
3. Fit MRI data
3.a. Load input data
This section shows how you can load data into a(n) mp2rage object.
- At the CLI level, qMRLab accepts structs containing (double) data in the fields named in accordance with a qMRLab model.
See the generic notes section below for BIDS compatible wrappers and scalable
% |- mp2rage object needs 7 data input(s) to be assigned: % |- MP2RAGE % |- INV1mag % |- INV1phase % |- INV2mag % |- INV2phase % |- B1map % |- Mask data = struct(); % MP2RAGE.mat contains [143 218 2] data. load('mp2rage_data/MP2RAGE.mat'); % B1map.mat contains [143 218 2] data. load('mp2rage_data/B1map.mat'); data.MP2RAGE= double(MP2RAGE); data.B1map= double(B1map);
3.b. Execute fitting process
This section will fit the loaded data.
FitResults = FitData(data,Model,0);
Visit the generic notes section below for instructions to accelerate fitting by
3.c. Display FitResults
You can display the current outputs by:
A representative fit curve will be plotted if available.
To render images in this page, we will load the fit results that had been saved before. You can skip the following code block;
% Load FitResults that comes with the example dataset. FitResults_old = load('FitResults/FitResults.mat'); qMRshowOutput(FitResults_old,data,Model);
3.d. Save fit results
Outputs can be saved as *.nii.(gz) if NIfTI inputs are available:
% Generic function call to save nifti outputs FitResultsSave_nii(FitResults, 'reference/nifti/file.nii.(gz)');
If not, FitResults.mat file can be saved. This file contains all the outputs as workspace variables:
% Generic function call to save FitResults.mat FitResultsSave_mat(FitResults);
FitResults.mat files can be loaded to qMRLab
GUI for visualization and ROI
The section below will be dynamically generated in accordance with the example data format (mat or nii). You can substitute FitResults_old with FitResults if you executed the fitting using example dataset for this model in section 3.b..
3.e. Re-use or share fit configuration files
qMRLab's fit configuration files (mp2rage_Demo.qmrlab.mat) store all the options and protocol in relation to the used model and the release version.
*.qmrlab.mat files can be easily shared with collaborators to allow them fit their own
data or run simulations using identical
4.a. Single Voxel Curve
Simulates single voxel curves
Not available for the current model.
4.b. Sensitivity Analysis
Simulates sensitivity to fitted parameters
Not available for the current model.
5.a. Notes specific to mp2rage
|== sub-01/ |~~~~~~ anat/ |---------- sub-01_inv-1_MP2RAGE.json |---------- sub-01_inv-1_part-mag_MP2RAGE.nii.gz |---------- sub-01_inv-1_part-phase_MP2RAGE.nii.gz |---------- sub-01_inv-2_MP2RAGE.json |---------- sub-01_inv-2_part-mag_MP2RAGE.nii.gz |---------- sub-01_inv-2_part-phase_MP2RAGE.nii.gz | |== derivatives/ |~~~~~~ Siemens/ |---------- dataset_description.json |~~~~~~~~~~ sub-01/anat/ |-------------- sub-01_UNIT1.nii.gz (Vendor-generated UNIT1) |-------------- sub-01_UNIT1.json |~~~~~~ qMRLab/ |---------- dataset_description.json |~~~~~~~~~~ sub-01/anat/ |-------------- sub-01_T1map.nii.gz |-------------- sub-01_T1map.json |-------------- sub-01_R1map.nii.gz |-------------- sub-01_R1map.json |-------------- sub-01_UNIT1.nii.gz (If calculated by qMRLab) |-------------- sub-01_UNIT1.json
For further information, please visit BIDS qMRI Appendix.
Further details about mp2rage protocol settings are available here.
Original repository: https://github.com/JosePMarques/MP2RAGE-related-scripts
5.b. Generic notes
5.b.1. Batch friendly option and protocol conventions
If you would like to load a desired set of options / protocols programatically, you can use *.qmrlab.mat files. To save a configuration from the protocol panel of mp2rage, first open the respective panel by running the following command in your MATLAB command window (MATLAB only):
In this panel, you can arrange available options and protocols according to your needs, then click the save button to save my_mp2rage.qmrlab.mat file. This file can be later loaded into a mp2rage object in batch by:
Model = mp2rage; Model = Model.loadObj('my_mp2rage.qmrlab.mat');
Model.loadObj('my_mp2rage.qmrlab.mat') call won't update the fields in the
Model object, unless the output is assigned to the object as shown above. This compromise on convenience is to retain Octave CLI compatibility.
If you don't have MATLAB, hence cannot access the GUI, two alternatives are available to populate options:
- Use qmrlab/mcrgui:latest Docker image to access GUI. The instructions are available here.
- Set options and protocols in CLI:
- List available option fields using tab completion in Octave's command prompt (or window)
Model = mp2rage; Model.option. % click the tab button on your keyboard and list the available fields.
- Assign the desired field. For example, for a mono_t2 object:
Model = mono_t2; Model.options.DropFirstEcho = true; Model.options.OffsetTerm = false;
Some option fields may be mutually exclusive or interdependent. Such cases are handled by the
GUI options panel; however, not exposed to the
CLI. Therefore, manual
options assignments may be challenging for some involved methods such as
qsm_sb. If above options are not working for you and you cannot infer how to set options solely in batch, please feel free to open an issue in qMRLab and request the protocol file you need.
Similarly, in CLI, you can inspect and assign the protocols:
Model = mp2rage; Model.Prot. % click the tab button on your keyboard and list the available fields.
Each protocol field has two subfields of Format and Mat. The first one is a cell indicating the name of the protocol parameter (such as EchoTime (ms)) and the latter one contains the respective values (such as 30 x 1 double array containing EchoTimes).
Mat protocol values are set according to the example datasets served via OSF.
The current model does not perform voxelwise fitting. Therefore, parallelization is not enabled.
qMRLab JOSS article
Karakuzu A., Boudreau M., Duval T.,Boshkovski T., Leppert I.R., Cabana J.F., Gagnon I., Beliveau P., Pike G.B., Cohen-Adad J., Stikov N. (2020), qMRLab: Quantitative MRI analysis, under one umbrella 10.21105/joss.02343
Reference article for mp2rage
Quantitative MRI, under one umbrella.
NeuroPoly Lab, Montreal, Canada