Beginners example with GUI

This will guide you step by step in processing a sample dataset with the user interface.

1. Open matlab

2. Run startup

Go to qMRLab installation folder (note: replace “PATH_QMRLAB” with the actual path)

cd PATH_QMRLAB

Setup your path (note: you only need to do it once)

startup

3. Download example data

In this case we will be working with Variable Flip Angle Data to compute a T1map. The main input data is stored as a 4D volume, where the 4th dimension is different flip angles. For example, in this test dataset, 1 slice at 2 different flip angles were acquired: volume 1 was FA=3degrees and volumes 2 was FA=20degrees, such that VFAData.nii.gz is 128x128x1x2. The other optional inputs are a Mask.nii.gz and a B1Map.nii.gz.

Run this in matlab to get the data:

Model=vfa_t1;
downloadData(Model,[])

When prompted, select a folder where you would like to put the sample data

4. Launch the GUI

Type this is matlab to launch the main GUI:

qMRLab

5. Model Selection

On the top left-hand side pull-down menu, select the method we are going to use, in this case, vfa_t1 (T1_relaxometry/) :

_images/method-select.png

At any time, you may use the Help button in the Options panel to get a description of the model:

_images/help.png

For the list of available models, please check Methods available

6. Load the data

Load the raw data in qMRLab by selecting Browse next to Work Dir. Select the folder where you have previously saved the sample data (this will load all the data into the correct locations automatically):

_images/load-data.png

For a more detailed description of what the input data should look like, please refer to 4.1 Data format

7. View the data

You can look at your data by clicking View next to the name of the file:

_images/view-data.png

You can browse through slices or volumes of the data files by using arrows and mouse controls. Please refer to 3. Data Viewer.

8. Set up the protocol

For this dataset, the protocol will be set up by default with the flip angles and TRs:

_images/protocol.png

For your own acquisition, you will have to use an external txt file to load the parameters, please refer to 6.1 Protocol.

9. View the data fit in 1 voxel

Before fitting the whole volume, it’s a good idea to take a look at your data and how it fits the model. Here, we can visualize the fit in 1 voxel at a time. In the Cursor section, press Select. Then select a voxel in the image and the press View data fit:

_images/select-vox.png

A new window will pop-up with the results of the fit in that voxel:

_images/fit.png

10. Fit the whole dataset

We can now fit the whole volume by pressing the large Fit Data button.

_images/fit-data.png

A wait bar will appear while the data is being processed and will automatically when done. From the pull-down menu to the left of the image, it’s possible to select the output you would like to view. For example, the T1map:

_images/view-fit.png

For more information and to explore other functionality such as the simulations, please visit Graphical User Interface Usage.