Chapter #four: The CONN GUI¶

Overview¶

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

As with an fMRI packet like SPM, though, the reliance on the GUI comes at the expense of flexibility. In a afterwards module on scripting we will run across how to write Matlab code that allows you lot to batch certain analyses and admission data that isn't available from the interface. Regardless, for most purposes the CONN GUI works very well, and newcomers will find it easy to learn.

Creating a New Projection¶

The first step of any CONN analysis is to create a new projection. This generates a Matlab structure that contains fields reflecting all aspects of the experiment that have been changed from the GUI, such as options, names of files, and what information has been loaded. Allow'southward say, for case, that nosotros click on the New push button and proper name our project conn_Arithmetic_Project . Save it into the CONN_Demo folder, and so go back to the Matlab terminal. Navigate to that binder, and notice that it now contains a .mat file chosen conn_Arithmetic_Project.mat . You tin load this file in the Matlab terminal by typing:

                                    load                  conn_Arithmetic_Project

In that location is now a new variable in your workspace called CONN_x . This is a construction file that contains all of the fields of your experiment, similar to how a job file in SPM contains information on all of the changes you made in the GUI. In the figure below, I have already filled in a few of the fields in the GUI, such every bit the RT, number of subjects, and FWHM:

../../_images/04_CONN_MatFile.png

Note

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

As yous make changes to the project during preprocessing and certain analyses, you can overwrite the project file at any time by hovering your cursor over the "Project" menu and selecting "Salve As". You can then close the CONN GUI if you lot need to, re-open up it at a later time, and load your project by clicking the "Open" 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 most of the buttons in darker shades. If you prefer some other layout, you lot can change the appearance of the GUI in society to arrive easier to read. Hover your mouse over the "Tools" carte, and select "GUI options." This will open a window that allows yous to do things like increment the font size or change the color scheme. A couple of other usually used options are:

  1. "Enable help tips", which allows yous to choose whether to take 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 detail step, merely if you find the help bubble distracting, you can hide information technology.
  2. The "Background anatomical epitome" and "Background reference atlas" options allow you to specify the template that is used to project your results onto; you will see how the results are displayed once we cover 1st-level analysis, and if you don't like the default reference volume, you can cull a different one.

../../_images/04_GUI_Options.png

There are many other options likewise these, and you are encouraged to attempt others out to adjust your tastes. These won't affect your results, but they can make doing the analysis easier and more pleasant to exercise; and after all, why make life more than difficult than it needs to be?

The Setup Tab¶

The CONN GUI is framed by a strip of tabs running forth the top of the window, and a cavalcade 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 information in that workspace.

The tabs at the top of the window, from left to right, represent each of the steps that will demand to be washed in society to analyze a resting-country dataset:

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

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

In this experiment in that location was one resting-land scan and one anatomical scan per subject; since we are beginning by analyzing just 1 subject, 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, we learn that the Repetition Time (i.due east., the TR) was 3.56 seconds; enter this number in the "Repetition Time (seconds)" field.

The "Acquisition type" field provides ii choices: Continuous and Sparse . About experiments will use Continuous conquering; Sparse acquisition is used for consequence-related designs, and omits convolving the HRF with the onset of each trial. For now, leave information technology as the default of Continuous .

../../_images/04_Basic.png

The Structural Tab¶

We at present move down the left side of the GUI to the "Structural" tab. Click on it, and and then apply 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 "one file has been assigned to 1 subject". Click OK, and the structural image will be loaded in the eye window.

Whenever you load information into the CONN toolbox, and whenever you accept generated an output file after processing the data you have loaded, it is good exercise to look at your data. This means examining the data yous loaded to make certain there are no artifacts and no irregularities, such as flipped orientations or Gibbs ringing artifacts. One time the data is loaded y'all can use slider to the right of the epitome to flip through different slices, and the "o" button at the top of the slider will alter the viewing montage between axial, coronal, and sagittal slices. Left-clicking on the slices themselves will open upwards another display window that allows you lot to wait at the slices in multiple planes by clicking multiple checkboxes - for example, in the x and y, or x, y, and z dimensions.

../../_images/04_Anatomical_Display.png

Clicking on the structural slices in the CONN GUI will open up another display window that allows y'all to view the slices in iii 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 heart window. The outset volume in the time-serial is displayed on the left, and the terminal volume in the fourth dimension-serial is displayed on the right; if there was any major movement or artifacts between the beginning and the end of the time-series, it would bear witness up in this side-by-side comparison. If at that place was piffling or no move and no artifacts, on the other hand, the two images should await well-nigh identical.

As with the Structural tab, y'all can switch between viewing planes and flip betwixt different slices of the functional data. There is a divergence, however: Instead of opening upwardly a new viewing window, clicking on the slices will open up a time-series plot, extracted from the voxel that you clicked on. Since these data oasis't been preprocessed yet, you may notice trends in the direction of the time-series either upwards or downwards; these correspond scanner drift artifacts which are corrected past filtering out linear and college-lodge trends from the data.

../../_images/04_Functional_Display.png

A useful QA check to do at this phase is to click on the - functional tools: menu in the lesser left corner of the Functional data window, and select Piece 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 yellow. Check this to brand sure that the boundaries of the gyri and sulci of the functional data roughly match upwards with those of the anatomical image. Selecting both the coronal and axial planes is a good manner to make certain the ventricles and other internal structures are aligned.

../../_images/04_Functional_Anatomical_CheckReg.png

If you like, you can do the same QA check with the SPM Check Reg function by clicking the - functional tools: menu and selecting Display functional/anatomical coregistration (SPM) . This will open the Bank check Reg window, similar to what you used in the SPM tutorial.

Note

In that location are other options in the - functional tools: menu; look at each of them and guess what they do. Why would it not make sense at this time to look at the coregistration with the MNI boundaries?

Video¶

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

Next Steps¶

At that place are other options in the GUI, such as ROIs, Conditions, and Covariates. Nosotros will leave those for now, coming dorsum to them subsequently nosotros have preprocessed our data - which we turn to in the next affiliate.