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Chapter #4: The CONN GUI¶

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Overview¶

One of CONN'south major advantages is its graphical user interface (GUI). Virtually everything that you will need to practise can be done from the GUI, and CONN's layout is straightforward and clear.

As with an fMRI package similar SPM, though, the reliance on the GUI comes at the expense of flexibility. In a afterward module on scripting we will see how to write Matlab lawmaking that allows yous to batch certain analyses and access data that isn't available from the interface. Regardless, for most purposes the CONN GUI works very well, and newcomers will find it piece of cake to acquire.

Creating a New Project¶

The first pace of any CONN analysis is to create a new project. This generates a Matlab structure that contains fields reflecting all aspects of the experiment that have been inverse from the GUI, such as options, names of files, and what data has been loaded. Permit'south say, for example, that we click on the New button and proper noun our project conn_Arithmetic_Project . Save it into the CONN_Demo folder, and so get back to the Matlab final. Navigate to that folder, and notice that it now contains a .mat file called conn_Arithmetic_Project.mat . Yous can load this file in the Matlab terminal by typing:

                                    load                  conn_Arithmetic_Project                

There is now a new variable in your workspace called CONN_x . This is a structure file that contains all of the fields of your experiment, like to how a job file in SPM contains data on all of the changes you lot fabricated in the GUI. In the figure below, I have already filled in a few of the fields in the GUI, such equally the RT, number of subjects, and FWHM:

Notation

Those with experience using SPM may observe it useful to review the chapter on scripting in SPM. The concepts are similar, and the newcomer to CONN may find information technology easier to sympathize what the .mat file does once he reviews how the same idea is carried out in SPM.

As you make changes to the project during preprocessing and certain analyses, you can overwrite the projection file at any time by hovering your cursor over the "Projection" menu and selecting "Save Equally". You tin so close the CONN GUI if you need to, re-open information technology at a later time, and load your project past clicking the "Open up" button and selecting the project file that yous created.

Other Options¶

The default appearance of the CONN toolbox is a black background with white text, and well-nigh of the buttons in darker shades. If y'all prefer some other layout, you can change the advent of the GUI in club to brand information technology easier to read. Hover your mouse over the "Tools" carte du jour, and select "GUI options." This will open up a window that allows y'all to do things like increment the font size or change the colour scheme. A couple of other commonly used options are:

1. "Enable aid tips", which allows you to choose whether to have CONN automatically display help text when you hover your mouse over certain options. This is useful for displaying all of the options that are associated with a particular stride, just if you find the help bubble distracting, you tin can hide it.
2. The "Background anatomical prototype" and "Background reference atlas" options let you to specify the template that is used to projection your results onto; you will see how the results are displayed once we cover 1st-level assay, and if you don't like the default reference volume, y'all can choose a unlike i.

There are many other options besides these, and you are encouraged to try others out to suit your tastes. These won't affect your results, but they tin make doing the assay easier and more than pleasant to practise; and after all, why make life more difficult than it needs to be?

The Setup Tab¶

The CONN GUI is framed by a strip of tabs running along the top of the window, and a column of buttons on the left side. These tabs and buttons control what is seen in the working space of the GUI, and what will be done to the data in that workspace.

The tabs at the top of the window, from left to correct, represent each of the steps that will need to be done in lodge to clarify a resting-state dataset:

1. Setup
2. Denoising
3. Analyses (1st-level)
4. Results (second-level)

To begin our bout of the CONN GUI we will focus on the Setup tab, which is where you volition enter the scanning parameters for the study - such as the number of runs and the TR. There are as well buttons for loading the structural and functional images. Once these images are loaded, we can then begin to preprocess the data, which we volition discuss in the next affiliate.

In this experiment at that place was one resting-state scan and one anatomical browse per subject; since nosotros are start past analyzing just one subject field, nosotros enter i for the "Number of subjects" field, and 1 for the "Number of sessions or runs" field. From the sub-01_task-rest_bold.json on the Openneuro data download page, nosotros learn that the Repetition Time (i.e., the TR) was iii.56 seconds; enter this number in the "Repetition Time (seconds)" field.

The "Acquisition blazon" field provides 2 choices: Continuous and Sparse . Most experiments will use Continuous acquisition; Sparse conquering is used for outcome-related designs, and omits convolving the HRF with the onset of each trial. For at present, get out it equally the default of Continuous .

The Structural Tab¶

Nosotros now movement down the left side of the GUI to the "Structural" tab. Click on it, and then employ the carte du jour on the right-hand side of the GUI to select the file sub-01_anat_sub-01_T1w.nii . A pop-up window will say that "1 file has been assigned to one subject". Click OK, and the structural prototype volition be loaded in the center window.

Whenever you load data into the CONN toolbox, and whenever yous have generated an output file afterwards processing the data you take loaded, it is adept practice to expect at your information. This means examining the information you loaded to make sure in that location are no artifacts and no irregularities, such as flipped orientations or Gibbs ringing artifacts. Once the information is loaded you can use slider to the correct of the prototype to flip through different slices, and the "o" button at the top of the slider volition change the viewing montage betwixt axial, coronal, and sagittal slices. Left-clicking on the slices themselves will open up another display window that allows you to await at the slices in multiple planes past clicking multiple checkboxes - for case, in the x and y, or x, y, and z dimensions.

Clicking on the structural slices in the CONN GUI will open up some other display window that allows y'all to view the slices in three dimensions.

The Functional Tab¶

The Functional tab is similar to the structural tab - select the file sub-01_func_sub-01_task-rest_bold.nii , and it will load the paradigm's slices into the center window. The commencement book in the time-series is displayed on the left, and the last volume in the fourth dimension-series is displayed on the correct; if at that place was any major movement or artifacts between the beginning and the end of the time-series, information technology would show upwards in this side-by-side comparison. If there was little or no motion and no artifacts, on the other mitt, the ii images should look about identical.

As with the Structural tab, you can switch between viewing planes and flip between different slices of the functional data. There is a difference, notwithstanding: Instead of opening upward a new viewing window, clicking on the slices will open a time-series plot, extracted from the voxel that y'all clicked on. Since these data haven't been preprocessed however, you may notice trends in the direction of the fourth dimension-series either upwardly or downwards; these represent scanner drift artifacts which are corrected by filtering out linear and higher-lodge trends from the data.

A useful QA check to do at this phase is to click on the - functional tools: bill of fare in the bottom left corner of the Functional data window, and select Slice viewer with anatomical overlay (QA_REG) . This displays the functional data and anatomical image simultaneously, and traces out the major sulcal and gyral curves in yellowish. Check this to brand certain that the boundaries of the gyri and sulci of the functional data roughly match upward with those of the anatomical epitome. Selecting both the coronal and axial planes is a good way to make certain the ventricles and other internal structures are aligned.

If you similar, yous tin do the same QA bank check with the SPM Cheque Reg office by clicking the - functional tools: menu and selecting Brandish functional/anatomical coregistration (SPM) . This volition open the Bank check Reg window, similar to what yous used in the SPM tutorial.

Note

There are other options in the - functional tools: carte; look at each of them and approximate what they do. Why would it not make sense at this time to await at the coregistration with the MNI boundaries?

Video¶

For a video overview of the CONN GUI, click hither.

Next Steps¶

There are other options in the GUI, such every bit ROIs, Atmospheric condition, and Covariates. We will exit those for now, coming back to them after nosotros have preprocessed our data - which we turn to in the next affiliate.

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Source: https://andysbrainbook.readthedocs.io/en/latest/FunctionalConnectivity/CONN_ShortCourse/CONN_04_GUI_Overview.html