Image Reconstruction - BUNPC/AtlasViewer GitHub Wiki

NOTE that these instructions assume that you have already generated sensitivity profile. If not please see the instructions on generating sensitivity profile.

A group-level directory folder should contain a subfolder for each subject, the original SD file, and groupResult.mat file. Each subject folder should contain the .nirs data file, digpt.txt file, and atlasViewer.mat created for that subject. An fw folder and imagerecon folder will also be created automatically by AtlasViewer and stored in the subject folder.

In this example as shown below, we have a group folder that contains the Probe.SD file, groupResult.mat file, Subj1 subfolder, and Subj2 subfolder. Each subfolder has a digpt.txt file containing 3D coordinates of all sources, all detectors and five landmarks, also contains an atlasViewer.mat file and NIRS data file (i.e., subj1.nirs and subj2.nirs).

(1) Open AtlasViewerGUI in the group folder. Group Subject List will appear as a second window, as shown below. Note that this happens only when you have groupResults.mat in the group directory.



(2) Go to Subj1 from the Group Subject List window.



Go to Tools --> Register Atlas to Dig Points, then click the Register Probe to Surface.




Go to Forward Model --> Load Precalculated Profile.



Then go to File --> Save Viewer State. This will help AtlasViewer recognize the latest state, i.e., registered Atlas with sensitivity.



(3) Go to Subj2 from the Group Subject List window, and repeat the step (2) for Subj 2.

(4) After that, the user could reconstruct images for Subj1 and Subj2. Here we do the next steps for Subj2 as an example. Open Image Recon GUI using Image Recon --> Image Recon GUI.



(5) This will open the Image Recon GUI as shown in the following figures.

• Choose the BRAIN ONLY option.
• Choose experimental condition. This number should match with the order of conditions in your .nirs file. In this example, we have only one condition: finger tapping.
• Choose the time range when you expect the peak response. In this example, finger tapping was from 0-5 sec, and the expected peak response was from 5-10 sec.
  
  

• Set regularization parameter. We use the default value alpha=0.01 in this example.
• Set the short separation threshold. This is in case short separations were not digitalized. Keep default 0.
  
  

(6) Click the Reconstruct Image button, then click the Plot Image button to visualize HbO/HbR.

(7) After that, images of HbO/HbR will be displayed in AtlasViewer GUI, as shown below.
The user could go the Image Display dropdown menu to switch between HbO Recon/ HbR Recon. The user could also uncheck the “Head” radio button, hide probe, and hide measurement list to get a better view.

(1) Go back to the group directory from the Group Subject List window or from “File --> Change Subject.”

(2) Go to the Tools --> Import Probe and choose the SD file (i.e., the probe.SD in this example). Then click the Register Probe to Surface.

(3) Load sensitivity profile using the menu Forward Model --> Load Precalculated Profile.

(4) Go to the menu File --> Save Viewer State.

(5) Run Image Recon GUI for group using Image Recon --> Image Recon GUI. Choose BRAIN ONLY. Then click Reconstruct Image and Plot Image.

(6) After that, the HbO Recon/ HbR Recon, OR the Sensitivity result for group could be displayed from the Image Display dropdown menu.

Before displaying HbO/HbR overlay, please first make sure to create groupResults.mat by analyzing your data using HOMER.

(1) Go to the folder you have the groupResults.mat file (i.e., the Group directory folder in this example) and launch AtlasViewerGUI.

(2) Go to the Tools --> Import Probe and choose the SD file (i.e., the probe.SD in this example). Then click the Register Probe to Surface.

(3) Go to the Tools --> Select Hb Conc Overlay, select trange (the time range of HRF that you want to take the mean of the dataset).

(4) Select HbOConc/HbRConc from the Image Display menu.

Before the next steps, please first register atlas to digpts from “Tools --> Register Atlas to digpts,” register the probe to surface from “Register Probe to Surface,” and load the precalculated profile from “Forward Model --> Load Precalculated Profile.”

If the user has already done the above steps,
(1) Go to the Image Recon --> Calculate Image Metrics.
(2) Examine the parameter settings from the pop-up window and Click the OK button.
(3) The localization error results will be displayed, as shown below. Then set the colormap threshold to [0 15].



The user could go the Image Display dropdown menu and choose Resolution to view the resolution results.

After displaying the above images, the user could copy and save these figures using the Copy Image button.