fixes to build version 1.1.3

changelog.md

@@ -1,3 +1,22 @@
+# Version 1.1.3
+
+- Added back the ability to use the fOLD dataset. Fixes [Issue 23](https://git.research.dezeeuw.ca/tyler/flares/issues/23)
+- 5th option has been added under Analysis to get to fOLD channels per participant
+- Added an option to cancel the running process. Fixes [Issue 15](https://git.research.dezeeuw.ca/tyler/flares/issues/15)
+- Prevented graph images from showing when participants are being processed. Fixes [Issue 24](https://git.research.dezeeuw.ca/tyler/flares/issues/24)
+- Allow the option to remove all events of a type from all loaded snirfs. Fixes [Issue 25](https://git.research.dezeeuw.ca/tyler/flares/issues/25)
+- Added new icons in the menu bar
+- Added a terminal to interact with the app in a more command-like form
+- Currently the terminal has no functionality but some features for batch operations will be coming soon!
+- Inter-Group viewer now has the option to visualize the average response on the brain of all participants in the group. Fixes [Issue 26](https://git.research.dezeeuw.ca/tyler/flares/issues/24)
+
+
+# Version 1.1.2
+
+- Fixed incorrect colormaps being applied
+- Added functionality to utilize external event markers from a file. Fixes [Issue 6](https://git.research.dezeeuw.ca/tyler/flares/issues/6)
+
+
 # Version 1.1.1
 
 - Fixed the number of rectangles in the progress bar to 19

flares.py

@@ -55,7 +55,7 @@ import pyvistaqt # type: ignore
 
 # External library imports for mne
 from mne import (
-    EvokedArray, SourceEstimate, Info, Epochs, Label,
+    EvokedArray, SourceEstimate, Info, Epochs, Label, Annotations,
     events_from_annotations, read_source_spaces,
     stc_near_sensors, pick_types, grand_average, get_config, set_config, read_labels_from_annot
 )  # type: ignore
@@ -132,6 +132,8 @@ ENHANCE_NEGATIVE_CORRELATION: bool
 
 SHORT_CHANNEL: bool
 
+REMOVE_EVENTS: list
+
 VERBOSITY = True
 
 # FIXME: Shouldn't need each ordering - just order it before checking
@@ -179,6 +181,7 @@ REQUIRED_KEYS: dict[str, Any] = {
     "PSP_THRESHOLD": float,
     
     "SHORT_CHANNEL": bool,
+    "REMOVE_EVENTS": list,
     # "REJECT_PAIRS": bool,
     # "FORCE_DROP_ANNOTATIONS": list,
     # "FILTER_LOW_PASS": float,
@@ -1074,7 +1077,7 @@ def epochs_calculations(raw_haemo, events, event_dict):
 
     # Plot drop log
     # TODO: Why show this if we never use epochs2?
-    fig_epochs_dropped = epochs2.plot_drop_log()
+    fig_epochs_dropped = epochs2.plot_drop_log(show=False)
     fig_epochs.append(("fig_epochs_dropped", fig_epochs_dropped))
 
     # Plot for each condition
@@ -1470,9 +1473,15 @@ def resource_path(relative_path):
 
 def fold_channels(raw: BaseRaw) -> None:
 
+    # if getattr(sys, 'frozen', False):
+    path = os.path.expanduser("~") + "/mne_data/fOLD/fOLD-public-master/Supplementary"
+    logger.info(path)
+    set_config('MNE_NIRS_FOLD_PATH', resource_path(path)) # type: ignore
 
-    # Locate the fOLD excel files
+    # # Locate the fOLD excel files
-    set_config('MNE_NIRS_FOLD_PATH', resource_path("../../mne_data/fOLD/fOLD-public-master/Supplementary")) # type: ignore
+    # else:
+    #     logger.info("yabba")
+    #     set_config('MNE_NIRS_FOLD_PATH', resource_path("../../mne_data/fOLD/fOLD-public-master/Supplementary")) # type: ignore
 
     output = None
 
@@ -1534,8 +1543,8 @@ def fold_channels(raw: BaseRaw) -> None:
             "Brain_Outside",
         ]
 
-        cmap1 = plt.cm.get_cmap('tab20')  # First 20 colors
+        cmap1 = plt.get_cmap('tab20')  # First 20 colors
-        cmap2 = plt.cm.get_cmap('tab20b')  # Next 20 colors
+        cmap2 = plt.get_cmap('tab20b')  # Next 20 colors
 
         # Combine the colors from both colormaps
         colors = [cmap1(i) for i in range(20)] + [cmap2(i) for i in range(20)]  # Total 40 colors
@@ -1611,6 +1620,7 @@ def fold_channels(raw: BaseRaw) -> None:
     for ax in axes[len(hbo_channel_names):]:
         ax.axis('off')
     
+    plt.show()
     return fig, legend_fig
 
                 
@@ -2935,6 +2945,19 @@ def process_participant(file_path, progress_callback=None):
     logger.info("14")
 
     # Step 14: Design Matrix
+    events_to_remove = REMOVE_EVENTS
+        
+    filtered_annotations = [ann for ann in raw.annotations if ann['description'] not in events_to_remove]
+    
+    new_annot = Annotations(
+        onset=[ann['onset'] for ann in filtered_annotations],
+        duration=[ann['duration'] for ann in filtered_annotations],
+        description=[ann['description'] for ann in filtered_annotations]
+    )
+    
+    # Set the new annotations
+    raw_haemo.set_annotations(new_annot)
+
     design_matrix, fig_design_matrix = make_design_matrix(raw_haemo, short_chans)
     fig_individual["Design Matrix"] = fig_design_matrix
     if progress_callback: progress_callback(15)

icons/terminal_24dp_1F1F1F.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="24px" viewBox="0 -960 960 960" width="24px" fill="#1f1f1f"><path d="M160-160q-33 0-56.5-23.5T80-240v-480q0-33 23.5-56.5T160-800h640q33 0 56.5 23.5T880-720v480q0 33-23.5 56.5T800-160H160Zm0-80h640v-400H160v400Zm140-40-56-56 103-104-104-104 57-56 160 160-160 160Zm180 0v-80h240v80H480Z"/></svg>

icons/upgrade_24dp_1F1F1F.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="24px" viewBox="0 -960 960 960" width="24px" fill="#1f1f1f"><path d="M280-160v-80h400v80H280Zm160-160v-327L336-544l-56-56 200-200 200 200-56 56-104-103v327h-80Z"/></svg>

main.py

@@ -42,11 +42,14 @@ from PySide6.QtWidgets import (
 )
 from PySide6.QtCore import QThread, Signal, Qt, QTimer, QEvent, QSize
 from PySide6.QtGui import QAction, QKeySequence, QIcon, QIntValidator, QDoubleValidator, QPixmap, QStandardItemModel, QStandardItem
+from PySide6.QtSvgWidgets import QSvgWidget # needed to show svgs when app is not frozen
 
 
 CURRENT_VERSION = "1.0.1"
 
 API_URL = "https://git.research.dezeeuw.ca/api/v1/repos/tyler/flares/releases"
+API_URL_SECONDARY = "https://git.research2.dezeeuw.ca/api/v1/repos/tyler/flares/releases"
+
 PLATFORM_NAME = platform.system().lower()
 
 # Selectable parameters on the right side of the window
@@ -143,6 +146,7 @@ SECTIONS = [
     {
         "title": "Design Matrix",
         "params": [
+            {"name": "REMOVE_EVENTS", "default": "None", "type": list, "help": "Remove events matching the names provided before generating the Design Matrix"},
             # {"name": "DRIFT_MODEL", "default": "cosine", "type": str, "help": "Drift model for GLM."},
             # {"name": "DURATION_BETWEEN_ACTIVITIES", "default": 35, "type": int, "help": "Time between activities (s)."},
             # {"name": "SHORT_CHANNEL_REGRESSION", "default": True, "type": bool, "help": "Use short channel regression."},
@@ -170,6 +174,58 @@ SECTIONS = [
 
 
 
+class TerminalWindow(QWidget):
+    def __init__(self, parent=None):
+        super().__init__(parent, Qt.WindowType.Window)
+        self.setWindowTitle("Terminal - FLARES")
+
+        self.output_area = QTextEdit()
+        self.output_area.setReadOnly(True)
+
+        self.input_line = QLineEdit()
+        self.input_line.returnPressed.connect(self.handle_command)
+
+        layout = QVBoxLayout()
+        layout.addWidget(self.output_area)
+        layout.addWidget(self.input_line)
+        self.setLayout(layout)
+
+        self.commands = {
+            "hello": self.cmd_hello,
+            "help": self.cmd_help
+        }
+
+    def handle_command(self):
+        command_text = self.input_line.text()
+        self.input_line.clear()
+
+        self.output_area.append(f"> {command_text}")
+        parts = command_text.strip().split()
+        if not parts:
+            return
+
+        command_name = parts[0]
+        args = parts[1:]
+
+        func = self.commands.get(command_name)
+        if func:
+            try:
+                result = func(*args)
+                if result:
+                    self.output_area.append(str(result))
+            except Exception as e:
+                self.output_area.append(f"[Error] {e}")
+        else:
+            self.output_area.append(f"[Unknown command] '{command_name}'")
+
+
+    def cmd_hello(self, *args):
+        return "Hello from the terminal!"
+
+    def cmd_help(self, *args):
+        return f"Available commands: {', '.join(self.commands.keys())}"
+    
+
 class UpdateDownloadThread(QThread):
     """
     Thread that downloads and extracts an update package and emits a signal on completion or error.
@@ -276,6 +332,10 @@ class UpdateCheckThread(QThread):
         return (normalize(v1) > normalize(v2)) - (normalize(v1) < normalize(v2))
 
     def get_latest_release_for_platform(self):
+        urls = [API_URL, API_URL_SECONDARY]
+        for url in urls:
+            try:
+                    
                 response = requests.get(API_URL, timeout=5)
                 response.raise_for_status()
                 releases = response.json()
@@ -291,7 +351,9 @@ class UpdateCheckThread(QThread):
                         return tag, asset["browser_download_url"]
 
                 return tag, None
-        
+            except (requests.RequestException, ValueError) as e:
+                continue
+        return None, None
 
 
 class LocalPendingUpdateCheckThread(QThread):
@@ -668,13 +730,12 @@ class UpdateEventsWindow(QWidget):
         self.description = QLabel()
         self.description.setTextFormat(Qt.TextFormat.RichText)
         self.description.setTextInteractionFlags(Qt.TextInteractionFlag.TextBrowserInteraction)
-        self.description.setOpenExternalLinks(False) # Handle the click internally
+        self.description.setOpenExternalLinks(True)
             
-        self.description.setText("Some software when creating snirf files will insert a template of optode positions as the correct position of the optodes for the participant.<br>"
+        self.description.setText("The events that are present in a snirf file may not be the events that are to be studied and examined.<br>"
-        "This is rarely correct as each head differs slightly in shape or size, and a lot of calculations require the optodes to be in the correct location.<br>"
+        "Utilizing different software and video recordings, it is easy enough to see when an action actually occured in a file.<br>"
-        "Using a .txt file, we can update the positions in the snirf file to match those of a digitization system such as one from Polhemus or elsewhere.<br>"
+        "The software <a href='https://www.boris.unito.it/'>BORIS</a> is used to add these events to video files, and these events can be applied to the snirf file <br>"
-        "The .txt file should have the fiducials, detectors, and sources clearly labeled, followed by the x, y, and z coordinates seperated by a space.<br>"
+        "selected below by selecting the correct BORIS observation and time syncing it to an event that it shares with the snirf file.")
-        "An example format of what a digitization text file should look like can be found <a href='custom_link'>by clicking here</a>.")
 
         layout.addWidget(self.description)
 
@@ -1113,6 +1174,11 @@ class ProgressBubble(QWidget):
             else:
                 rect.setStyleSheet("background-color: white; border: 1px solid gray;")
                 
+    def mark_cancelled(self):
+        if 0 <= self.current_step < len(self.rects):
+            rect = self.rects[self.current_step]
+            rect.setStyleSheet("background-color: red; border: 1px solid gray;")
+
     def mousePressEvent(self, event):
         self.clicked.emit(self)
         super().mousePressEvent(event)
@@ -1201,6 +1267,8 @@ class ParamSection(QWidget):
                 widget = QLineEdit()
                 widget.setValidator(QDoubleValidator())
                 widget.setText(str(param["default"]))
+            elif param["type"] == list:
+                widget = self._create_multiselect_dropdown(None)
             else: 
                 widget = QLineEdit()
                 widget.setText(str(param["default"]))
@@ -1216,6 +1284,81 @@ class ParamSection(QWidget):
                 "type": param["type"]
             }
 
+    def _create_multiselect_dropdown(self, items):
+        combo = FullClickComboBox()
+        combo.setView(QListView())
+        model = QStandardItemModel()
+        combo.setModel(model)
+        combo.setEditable(True)
+        combo.lineEdit().setReadOnly(True)
+        combo.lineEdit().setPlaceholderText("Select...")
+
+        dummy_item = QStandardItem("<None Selected>")
+        dummy_item.setFlags(Qt.ItemIsEnabled)
+        model.appendRow(dummy_item)
+
+        toggle_item = QStandardItem("Toggle Select All")
+        toggle_item.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
+        toggle_item.setData(Qt.Unchecked, Qt.CheckStateRole)
+        model.appendRow(toggle_item)
+
+        if items is not None:
+            for item in items:
+                standard_item = QStandardItem(item)
+                standard_item.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
+                standard_item.setData(Qt.Unchecked, Qt.CheckStateRole)
+                model.appendRow(standard_item)
+
+        combo.setInsertPolicy(QComboBox.NoInsert)
+
+
+        def on_view_clicked(index):
+            item = model.itemFromIndex(index)
+            if item.isCheckable():
+                new_state = Qt.Checked if item.checkState() == Qt.Unchecked else Qt.Unchecked
+                item.setCheckState(new_state)
+
+        combo.view().pressed.connect(on_view_clicked)
+
+        self._updating_checkstates = False
+
+        def on_item_changed(item):
+            if self._updating_checkstates:
+                return
+            self._updating_checkstates = True
+
+            normal_items = [model.item(i) for i in range(2, model.rowCount())]  # skip dummy and toggle
+
+            if item == toggle_item:
+                all_checked = all(i.checkState() == Qt.Checked for i in normal_items)
+                if all_checked:
+                    for i in normal_items:
+                        i.setCheckState(Qt.Unchecked)
+                    toggle_item.setCheckState(Qt.Unchecked)
+                else:
+                    for i in normal_items:
+                        i.setCheckState(Qt.Checked)
+                    toggle_item.setCheckState(Qt.Checked)
+
+            elif item == dummy_item:
+                pass
+
+            else:
+                # When normal items change, update toggle item
+                all_checked = all(i.checkState() == Qt.Checked for i in normal_items)
+                toggle_item.setCheckState(Qt.Checked if all_checked else Qt.Unchecked)
+                
+            self._updating_checkstates = False
+            
+            for param_name, info in self.widgets.items():
+                if info["widget"] == combo:
+                    self.update_dropdown_label(param_name)
+                    break
+
+        model.itemChanged.connect(on_item_changed)
+
+        combo.setInsertPolicy(QComboBox.NoInsert)
+        return combo
 
     def show_help_popup(self, text):
         msg = QMessageBox(self)
@@ -1232,6 +1375,8 @@ class ParamSection(QWidget):
 
             if expected_type == bool:
                 values[name] = widget.currentText() == "True"
+            elif expected_type == list:
+                values[name] = [x.strip() for x in widget.lineEdit().text().split(",") if x.strip()]
             else:
                 raw_text = widget.text()
                 try:
@@ -1241,9 +1386,6 @@ class ParamSection(QWidget):
                         values[name] = float(raw_text)
                     elif expected_type == str:
                         values[name] = raw_text
-                    elif expected_type == list:
-                        # Very basic CSV parsing - fix?
-                        values[name] = [x.strip() for x in raw_text.split(",") if x.strip()]
                     else:
                         values[name] = raw_text  # Fallback
                 except Exception as e:
@@ -1251,6 +1393,155 @@ class ParamSection(QWidget):
 
         return values
     
+    def update_dropdown_items(self, param_name, new_items):
+        """
+        Updates the items in a multi-select dropdown parameter field.
+
+        Args:
+            param_name (str): The parameter name (must match one in self.widgets).
+            new_items (list): The new items to populate in the dropdown.
+        """
+        widget_info = self.widgets.get(param_name)
+        print("[ParamSection] Current widget keys:", list(self.widgets.keys()))
+
+        if not widget_info:
+            print(f"[ParamSection] No widget found for param '{param_name}'")
+            return
+
+        widget = widget_info["widget"]
+        if not isinstance(widget, FullClickComboBox):
+            print(f"[ParamSection] Widget for param '{param_name}' is not a FullClickComboBox")
+            return
+
+        # Replace the model on the existing widget
+        new_model = QStandardItemModel()
+
+        dummy_item = QStandardItem("<None Selected>")
+        dummy_item.setFlags(Qt.ItemIsEnabled)
+        new_model.appendRow(dummy_item)
+
+        toggle_item = QStandardItem("Toggle Select All")
+        toggle_item.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
+        toggle_item.setData(Qt.Unchecked, Qt.CheckStateRole)
+        new_model.appendRow(toggle_item)
+
+        for item_text in new_items:
+            item = QStandardItem(item_text)
+            item.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
+            item.setData(Qt.Unchecked, Qt.CheckStateRole)
+            new_model.appendRow(item)
+
+        widget.setModel(new_model)
+        widget.setView(QListView())  # Reset view to refresh properly
+
+        def on_view_clicked(index):
+            item = new_model.itemFromIndex(index)
+            if item.isCheckable():
+                new_state = Qt.Checked if item.checkState() == Qt.Unchecked else Qt.Unchecked
+                item.setCheckState(new_state)
+
+        widget.view().pressed.connect(on_view_clicked)
+
+        def on_item_changed(item):
+            if getattr(self, "_updating_checkstates", False):
+                return
+            self._updating_checkstates = True
+
+            normal_items = [new_model.item(i) for i in range(2, new_model.rowCount())]
+            if item == toggle_item:
+                all_checked = all(i.checkState() == Qt.Checked for i in normal_items)
+                for i in normal_items:
+                    i.setCheckState(Qt.Unchecked if all_checked else Qt.Checked)
+                toggle_item.setCheckState(Qt.Unchecked if all_checked else Qt.Checked)
+            else:
+                all_checked = all(i.checkState() == Qt.Checked for i in normal_items)
+                toggle_item.setCheckState(Qt.Checked if all_checked else Qt.Unchecked)
+
+            self._updating_checkstates = False
+            
+            for param_name, info in self.widgets.items():
+                if info["widget"] == widget:
+                    self.update_dropdown_label(param_name)
+                    break
+
+        new_model.itemChanged.connect(on_item_changed)
+        widget.lineEdit().setText("<None Selected>")
+        
+        
+    def _get_checked_items(self, combo):
+        checked = []
+        model = combo.model()
+        for i in range(model.rowCount()):
+            item = model.item(i)
+            if item.text() in ("<None Selected>", "Toggle Select All"):
+                continue
+            if item.checkState() == Qt.Checked:
+                checked.append(item.text())
+        return checked
+
+    def update_dropdown_label(self, param_name):
+        widget_info = self.widgets.get(param_name)
+        if not widget_info:
+            print(f"[ParamSection] No widget found for param '{param_name}'")
+            return
+
+        widget = widget_info["widget"]
+        if not isinstance(widget, FullClickComboBox):
+            print(f"[ParamSection] Widget for param '{param_name}' is not a FullClickComboBox")
+            return
+
+        selected = self._get_checked_items(widget)
+        if not selected:
+            widget.lineEdit().setText("<None Selected>")
+        else:
+            # You can customize how you display selected items here:
+            widget.lineEdit().setText(", ".join(selected))
+        
+    def update_annotation_dropdown_from_folder(self, folder_path):
+        """
+        Reads all EEG files in the given folder, extracts annotations using MNE,
+        and updates the dropdown for the `target_param` with the set of common annotations.
+
+        Args:
+            folder_param (str): The name of the parameter holding the folder path.
+            target_param (str): The name of the multi-select dropdown to update.
+        """
+        # folder_path_widget = self.widgets.get(folder_param, {}).get("widget")
+        # if not folder_path_widget:
+        #     print(f"[ParamSection] Folder path param '{folder_param}' not found.")
+        #     return
+
+        # folder_path = folder_path_widget.text().strip()
+        # if not os.path.isdir(folder_path):
+        #     print(f"[ParamSection] '{folder_path}' is not a valid directory.")
+        #     return
+
+        annotation_sets = []
+        for filename in os.listdir(folder_path):
+            full_path = os.path.join(folder_path, filename)
+            try:
+                raw = read_raw_snirf(full_path, preload=False, verbose="ERROR")
+                annotations = raw.annotations
+                if annotations is not None:
+                    labels = set(annotations.description)
+                    annotation_sets.append(labels)
+            except Exception as e:
+                print(f"[ParamSection] Skipping file '{filename}' due to error: {e}")
+
+        if not annotation_sets:
+            print(f"[ParamSection] No annotations found in folder '{folder_path}'")
+            return
+
+        # Get common annotations
+        common_annotations = set.intersection(*annotation_sets) if len(annotation_sets) > 1 else annotation_sets[0]
+        common_annotations = sorted(list(common_annotations))  # for consistent order
+
+        print(f"[ParamSection] Common annotations: {common_annotations}")
+
+        # Update the dropdown
+        
+        self.update_dropdown_items("REMOVE_EVENTS", common_annotations)
+
 
 class FullClickLineEdit(QLineEdit):
     def mousePressEvent(self, event):
@@ -1865,6 +2156,202 @@ class ParticipantBrainViewerWidget(QWidget):
 
 
 
+class ParticipantFoldChannelsWidget(QWidget):
+    def __init__(self, haemo_dict, cha_dict):
+        super().__init__()
+        self.setWindowTitle("FLARES Participant Fold Channels Viewer")
+        self.haemo_dict = haemo_dict
+        self.cha_dict = cha_dict
+
+        # Create mappings: file_path -> participant label and dropdown display text
+        self.participant_map = {}  # file_path -> "Participant 1"
+        self.participant_dropdown_items = []  # "Participant 1 (filename)"
+
+        for i, file_path in enumerate(self.haemo_dict.keys(), start=1):
+            short_label = f"Participant {i}"
+            display_label = f"{short_label} ({os.path.basename(file_path)})"
+            self.participant_map[file_path] = short_label
+            self.participant_dropdown_items.append(display_label)
+
+        self.layout = QVBoxLayout(self)
+        self.top_bar = QHBoxLayout()
+        self.layout.addLayout(self.top_bar)
+
+        self.participant_dropdown = self._create_multiselect_dropdown(self.participant_dropdown_items)
+        self.participant_dropdown.currentIndexChanged.connect(self.update_participant_dropdown_label)
+              
+        self.index_texts = [
+            "0 (Fold Channels)",
+            # "1 (second image)",
+            # "2 (third image)",
+            # "3 (fourth image)",
+            ]
+
+        self.image_index_dropdown = self._create_multiselect_dropdown(self.index_texts)
+        self.image_index_dropdown.currentIndexChanged.connect(self.update_image_index_dropdown_label)
+
+        self.submit_button = QPushButton("Submit")
+        self.submit_button.clicked.connect(self.show_fold_images)
+
+        self.top_bar.addWidget(QLabel("Participants:"))
+        self.top_bar.addWidget(self.participant_dropdown)
+        self.top_bar.addWidget(QLabel("Fold Type:"))
+        self.top_bar.addWidget(self.image_index_dropdown)
+        self.top_bar.addWidget(QLabel("This will cause the app to hang for ~30s!"))
+        self.top_bar.addWidget(self.submit_button)
+
+        self.scroll = QScrollArea()
+        self.scroll.setWidgetResizable(True)
+        self.scroll_content = QWidget()
+        self.grid_layout = QGridLayout(self.scroll_content)
+        self.scroll.setWidget(self.scroll_content)
+        self.layout.addWidget(self.scroll)
+
+        self.thumb_size = QSize(280, 180)
+        self.showMaximized()
+
+    def _create_multiselect_dropdown(self, items):
+        combo = FullClickComboBox()
+        combo.setView(QListView())
+        model = QStandardItemModel()
+        combo.setModel(model)
+        combo.setEditable(True)
+        combo.lineEdit().setReadOnly(True)
+        combo.lineEdit().setPlaceholderText("Select...")
+
+
+        dummy_item = QStandardItem("<None Selected>")
+        dummy_item.setFlags(Qt.ItemIsEnabled)
+        model.appendRow(dummy_item)
+
+        toggle_item = QStandardItem("Toggle Select All")
+        toggle_item.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
+        toggle_item.setData(Qt.Unchecked, Qt.CheckStateRole)
+        model.appendRow(toggle_item)
+
+        for item in items:
+            standard_item = QStandardItem(item)
+            standard_item.setFlags(Qt.ItemIsUserCheckable | Qt.ItemIsEnabled)
+            standard_item.setData(Qt.Unchecked, Qt.CheckStateRole)
+            model.appendRow(standard_item)
+
+        combo.setInsertPolicy(QComboBox.NoInsert)
+
+
+        def on_view_clicked(index):
+            item = model.itemFromIndex(index)
+            if item.isCheckable():
+                new_state = Qt.Checked if item.checkState() == Qt.Unchecked else Qt.Unchecked
+                item.setCheckState(new_state)
+
+        combo.view().pressed.connect(on_view_clicked)
+
+        self._updating_checkstates = False
+
+        def on_item_changed(item):
+            if self._updating_checkstates:
+                return
+            self._updating_checkstates = True
+
+            normal_items = [model.item(i) for i in range(2, model.rowCount())]  # skip dummy and toggle
+
+            if item == toggle_item:
+                all_checked = all(i.checkState() == Qt.Checked for i in normal_items)
+                if all_checked:
+                    for i in normal_items:
+                        i.setCheckState(Qt.Unchecked)
+                    toggle_item.setCheckState(Qt.Unchecked)
+                else:
+                    for i in normal_items:
+                        i.setCheckState(Qt.Checked)
+                    toggle_item.setCheckState(Qt.Checked)
+
+            elif item == dummy_item:
+                pass
+
+            else:
+                # When normal items change, update toggle item
+                all_checked = all(i.checkState() == Qt.Checked for i in normal_items)
+                toggle_item.setCheckState(Qt.Checked if all_checked else Qt.Unchecked)
+
+            # Update label text immediately after change
+            if combo == self.participant_dropdown:
+                self.update_participant_dropdown_label()
+            elif combo == self.image_index_dropdown:
+                self.update_image_index_dropdown_label()
+
+            self._updating_checkstates = False
+
+        model.itemChanged.connect(on_item_changed)
+
+        combo.setInsertPolicy(QComboBox.NoInsert)
+        return combo
+    
+    def _get_checked_items(self, combo):
+        checked = []
+        model = combo.model()
+        for i in range(model.rowCount()):
+            item = model.item(i)
+            # Skip dummy and toggle items:
+            if item.text() in ("<None Selected>", "Toggle Select All"):
+                continue
+            if item.checkState() == Qt.Checked:
+                checked.append(item.text())
+        return checked
+
+    def update_participant_dropdown_label(self):
+        selected = self._get_checked_items(self.participant_dropdown)
+        if not selected:
+            self.participant_dropdown.lineEdit().setText("<None Selected>")
+        else:
+            # Extract just "Participant N" from "Participant N (filename)"
+            selected_short = [s.split(" ")[0] + " " + s.split(" ")[1] for s in selected]
+            self.participant_dropdown.lineEdit().setText(", ".join(selected_short))
+
+    def update_image_index_dropdown_label(self):
+        selected = self._get_checked_items(self.image_index_dropdown)
+        if not selected:
+            self.image_index_dropdown.lineEdit().setText("<None Selected>")
+        else:
+            # Only show the index part
+            index_labels = [s.split(" ")[0] for s in selected]
+            self.image_index_dropdown.lineEdit().setText(", ".join(index_labels))
+
+    def show_fold_images(self):
+        import flares
+
+        selected_display_names = self._get_checked_items(self.participant_dropdown)
+        selected_file_paths = []
+        for display_name in selected_display_names:
+            for fp, short_label in self.participant_map.items():
+                expected_display = f"{short_label} ({os.path.basename(fp)})"
+                if display_name == expected_display:
+                    selected_file_paths.append(fp)
+                    break
+
+        selected_indexes = [
+            int(s.split(" ")[0]) for s in self._get_checked_items(self.image_index_dropdown)
+        ]
+
+        # Pass the necessary arguments to each method
+        for file_path in selected_file_paths:
+            haemo_obj = self.haemo_dict.get(file_path)
+
+            if haemo_obj is None:
+                continue
+
+            #cha = self.cha_dict.get(file_path)
+
+            for idx in selected_indexes:
+                if idx == 0:
+
+                    flares.fold_channels(haemo_obj)
+
+                else:
+                    print(f"No method defined for index {idx}")
+
+
+
 class ClickableLabel(QLabel):
     def __init__(self, full_pixmap: QPixmap, thumbnail_pixmap: QPixmap):
         super().__init__()
@@ -2070,7 +2557,7 @@ class GroupViewerWidget(QWidget):
         self.index_texts = [
             "0 (GLM Results)",
             "1 (Significance)",
-            # "2 (third_image)",
+            "2 (Brain Activity Visualization)",
             # "3 (fourth image)",
             ]
 
@@ -2373,6 +2860,32 @@ class GroupViewerWidget(QWidget):
                     "type": float,
                 }
             ],
+            2: [
+                {
+                    "key": "show_optodes",
+                    "label": "Determine what is rendered above the brain. Valid values are 'sensors', 'labels', 'none', 'all'.",
+                    "default": "all",
+                    "type": str,
+                },
+                {
+                    "key": "t_or_theta",
+                    "label": "Specify if t values or theta values should be plotted. Valid values are 't', 'theta'",
+                    "default": "theta",
+                    "type": str,
+                },
+                {
+                    "key": "show_text",
+                    "label": "Display informative text on the top left corner. THIS DOES NOT WORK AND SHOULD BE LEFT AT FALSE",
+                    "default": "False",
+                    "type": bool,
+                },
+                {
+                    "key": "brain_bounds",
+                    "label": "Graph Upper/Lower Limit",
+                    "default": "1.0",
+                    "type": float,
+                }
+            ],
         }
 
         # Inject full_text from index_texts
@@ -2395,8 +2908,13 @@ class GroupViewerWidget(QWidget):
             
 
         all_cha = pd.DataFrame()
-        for fp in selected_file_paths:
+        for file_path in selected_file_paths:
-            cha_df = self.cha.get(fp)
+            haemo_obj = self.haemo_dict.get(file_path)
+
+            if haemo_obj is None:
+                continue
+            
+            cha_df = self.cha.get(file_path)
             if cha_df is not None:
                 all_cha = pd.concat([all_cha, cha_df], ignore_index=True)
 
@@ -2451,6 +2969,20 @@ class GroupViewerWidget(QWidget):
                 df_contrasts = pd.concat(all_contrasts, ignore_index=True)
                 flares.run_second_level_analysis(df_contrasts, p_haemo, p_val, graph_bounds)
 
+            elif idx == 2:
+                params = param_values.get(idx, {})
+                show_optodes = params.get("show_optodes", None)
+                t_or_theta = params.get("t_or_theta", None)
+                show_text = params.get("show_text", None)
+                brain_bounds = params.get("brain_bounds", None)
+
+                if show_optodes is None or t_or_theta is None or show_text is None or brain_bounds is None:
+                    print(f"Missing parameters for index {idx}, skipping.")
+                    continue
+
+                flares.brain_3d_visualization(haemo_obj, all_cha, selected_event, t_or_theta=t_or_theta, show_optodes=show_optodes, show_text=show_text, brain_bounds=brain_bounds)
+
+                
             elif idx == 3:
                 pass
 
@@ -3018,17 +3550,21 @@ class ViewerLauncherWidget(QWidget):
         btn2 = QPushButton("Open Participant Brain Viewer")
         btn2.clicked.connect(lambda: self.open_participant_brain_viewer(haemo_dict, cha_dict))
         
-        btn3 = QPushButton("Open Inter-Group Viewer")
+        btn3 = QPushButton("Open Participant Fold Channels Viewer")
-        btn3.clicked.connect(lambda: self.open_group_viewer(haemo_dict, cha_dict, df_ind, design_matrix, contrast_results_dict, group))
+        btn3.clicked.connect(lambda: self.open_participant_fold_channels_viewer(haemo_dict, cha_dict))
 
-        btn4 = QPushButton("Open Cross Group Brain Viewer")
+        btn4 = QPushButton("Open Inter-Group Viewer")
-        btn4.clicked.connect(lambda: self.open_group_brain_viewer(haemo_dict, df_ind, design_matrix, group, contrast_results_dict))
+        btn4.clicked.connect(lambda: self.open_group_viewer(haemo_dict, cha_dict, df_ind, design_matrix, contrast_results_dict, group))
+        
+        btn5 = QPushButton("Open Cross Group Brain Viewer")
+        btn5.clicked.connect(lambda: self.open_group_brain_viewer(haemo_dict, df_ind, design_matrix, group, contrast_results_dict))
 
 
         layout.addWidget(btn1)
         layout.addWidget(btn2)
         layout.addWidget(btn3)
         layout.addWidget(btn4)
+        layout.addWidget(btn5)
 
     def open_participant_viewer(self, haemo_dict, fig_bytes_dict):
         self.participant_viewer = ParticipantViewerWidget(haemo_dict, fig_bytes_dict)
@@ -3038,6 +3574,10 @@ class ViewerLauncherWidget(QWidget):
         self.participant_brain_viewer = ParticipantBrainViewerWidget(haemo_dict, cha_dict)
         self.participant_brain_viewer.show()
         
+    def open_participant_fold_channels_viewer(self, haemo_dict, cha_dict):
+        self.participant_fold_channels_viewer = ParticipantFoldChannelsWidget(haemo_dict, cha_dict)
+        self.participant_fold_channels_viewer.show()
+
     def open_group_viewer(self, haemo_dict, cha_dict, df_ind, design_matrix, contrast_results_dict, group):
         self.participant_brain_viewer = GroupViewerWidget(haemo_dict, cha_dict, df_ind, design_matrix, contrast_results_dict, group)
         self.participant_brain_viewer.show()
@@ -3063,9 +3603,12 @@ class MainApplication(QMainWindow):
         self.help = None
         self.optodes = None
         self.events = None
+        self.terminal = None
         self.bubble_widgets = {}
         self.param_sections = []
         self.folder_paths = []
+        self.section_widget = None
+        self.first_run = True
 
         self.init_ui()
         self.create_menu_bar()
@@ -3294,8 +3837,8 @@ class MainApplication(QMainWindow):
         options_actions = [
             ("User Guide", "F1", self.user_guide, resource_path("icons/help_24dp_1F1F1F.svg")), 
             ("Check for Updates", "F5", self.manual_check_for_updates, resource_path("icons/update_24dp_1F1F1F.svg")),
-            ("Update optodes in snirf file...", "F6", self.update_optode_positions, resource_path("icons/update_24dp_1F1F1F.svg")),
+            ("Update optodes in snirf file...", "F6", self.update_optode_positions, resource_path("icons/upgrade_24dp_1F1F1F.svg")),
-            ("Update events in snirf file...", "F7", self.update_event_markers, resource_path("icons/update_24dp_1F1F1F.svg")),
+            ("Update events in snirf file...", "F7", self.update_event_markers, resource_path("icons/upgrade_24dp_1F1F1F.svg")),
             ("About", "F12", self.about_window, resource_path("icons/info_24dp_1F1F1F.svg"))
         ]
 
@@ -3304,6 +3847,13 @@ class MainApplication(QMainWindow):
             if i == 1 or i == 3:  # after the first 2 actions (0,1)
                 options_menu.addSeparator()
 
+        terminal_menu = menu_bar.addMenu("Terminal")
+        terminal_actions = [
+            ("New Terminal", "Ctrl+Alt+T", self.terminal_gui, resource_path("icons/terminal_24dp_1F1F1F.svg")),
+        ]
+        for name, shortcut, slot, icon in terminal_actions:
+            terminal_menu.addAction(make_action(name, shortcut, slot, icon=icon))
+
         self.statusbar = self.statusBar()
         self.statusbar.showMessage("Ready")
 
@@ -3318,14 +3868,16 @@ class MainApplication(QMainWindow):
 
         # Add ParamSection widgets from SECTIONS
         for section in SECTIONS:
-            section_widget = ParamSection(section)
+            self.section_widget = ParamSection(section)
-            self.rows_layout.addWidget(section_widget)
+            self.rows_layout.addWidget(self.section_widget)
 
-            self.param_sections.append(section_widget)
+            self.param_sections.append(self.section_widget)
 
 
     def clear_all(self):
         
+        self.cancel_task()
+        
         self.right_column_widget.hide()
         
         # Clear the bubble layout
@@ -3386,6 +3938,11 @@ class MainApplication(QMainWindow):
             self.help = UserGuideWindow(self)
             self.help.show()
             
+    def terminal_gui(self):
+        if self.terminal is None or not self.terminal.isVisible():
+            self.terminal = TerminalWindow(self)
+            self.terminal.show()
+
     def update_optode_positions(self):
         if self.optodes is None or not self.optodes.isVisible():
             self.optodes = UpdateOptodesWindow(self)
@@ -3415,6 +3972,12 @@ class MainApplication(QMainWindow):
         if folder_path:
             self.selected_path = folder_path  # store the folder path
             self.show_files_as_bubbles(folder_path)
+            for section_widget in self.param_sections:
+                if "REMOVE_EVENTS" in section_widget.widgets:
+                    section_widget.update_annotation_dropdown_from_folder(folder_path)
+                    break
+            else:
+                print("[MainWindow] Could not find ParamSection with 'REMOVE_EVENTS' widget")
         
         self.button1.setVisible(True)
 
@@ -3724,8 +4287,52 @@ class MainApplication(QMainWindow):
         return self.file_metadata
 
 
+    def cancel_task(self):
+        self.button1.clicked.disconnect(self.cancel_task)
+        self.button1.setText("Stopping...")
+
+        if hasattr(self, "result_process") and self.result_process.is_alive():
+            parent = psutil.Process(self.result_process.pid)
+            children = parent.children(recursive=True)
+            for child in children:
+                try:
+                    child.kill()
+                except psutil.NoSuchProcess:
+                    pass
+            self.result_process.terminate()
+            self.result_process.join()
+
+        if hasattr(self, "result_timer") and self.result_timer.isActive():
+            self.result_timer.stop()
+        
+        # if hasattr(self, "result_process") and self.result_process.is_alive():
+        #     self.result_process.terminate()  # Forcefully terminate the process
+        #     self.result_process.join()       # Wait for it to properly close
+
+        # # Stop the QTimer if running
+        # if hasattr(self, "result_timer") and self.result_timer.isActive():
+        #     self.result_timer.stop()
+        
+        for bubble in self.bubble_widgets.values():
+            bubble.mark_cancelled()
+
+        self.statusbar.showMessage("Processing cancelled.")
+        self.button1.clicked.connect(self.on_run_task)
+        self.button1.setText("Process")
+
+
     '''MODULE FILE'''
     def on_run_task(self):
+        
+        self.button1.clicked.disconnect(self.on_run_task)
+        self.button1.setText("Cancel")
+        self.button1.clicked.connect(self.cancel_task)
+        
+        if not self.first_run:
+            for bubble in self.bubble_widgets.values():
+                bubble.mark_cancelled()
+        self.first_run = False
+
         # Collect all selected snirf files in a flat list
         snirf_files = []
 
@@ -4253,7 +4860,7 @@ def resource_path(relative_path):
         # PyInstaller bundle path
         base_path = sys._MEIPASS
     else:
-        base_path = os.path.abspath(".")
+        base_path = os.path.dirname(os.path.abspath(__file__))
 
     return os.path.join(base_path, relative_path)