gemprf 0.1.1__py3-none-any.whl

gem/__init__.py

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+from . import model
+from .model import *
+
+from . import tools
+from .tools import *
+
+from . import space
+from .space import *
+
+from .run_gem import run

gem/analysis/__init__.py

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+class my_class(object):
+    pass
+
+
+
+

gem/analysis/prf_analysis.py

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+# -*- coding: utf-8 -*-
+"""
+
+"@Author  :   Siddharth Mittal",
+"@Version :   1.0",
+"@Contact :   siddharth.mittal@meduniwien.ac.at",
+"@License :   (C)Copyright 2024, Medical University of Vienna",
+"@Desc    :   None",
+        
+"""
+
+import numpy as np
+import cupy as cp
+from typing import List
+
+from gem.model.prf_model import PRFModel
+from gem.model.selected_prf_model import SelectedPRFModel
+from gem.model.prf_stimulus import Stimulus
+from gem.space.PRFSpace import PRFSpace
+from gem.utils.hpc_cupy_utils import HpcUtils as gpu_utils
+
+  
+class PRFAnalysis():
+    def __init__(self, prf_space : PRFSpace, stimulus : Stimulus) -> None:
+        self.__prf_points = prf_space
+        self.__stimulus = stimulus
+        self.__model_signals_batches = None
+        self.__dervatives_signals_batches_list = None
+        self.__error_e = None
+        self.__error_de_dtheta_list = None # contains a list of all derivative errors w.r.t each parameter
+
+    @property
+    def prf_points(self)-> PRFSpace:
+        return self.__prf_points
+
+    @property
+    def stimulus(self)-> Stimulus:
+        return self.__stimulus
+
+    @property
+    def orthonormalized_S_batches(self)-> List[cp.ndarray]:
+        return self.__model_signals_batches
+    
+    @orthonormalized_S_batches.setter
+    def orthonormalized_S_batches(self, new_value)-> None:
+        self.__model_signals_batches = new_value
+
+    @property
+    def orthonormalized_dS_dtheta_batches_list(self)-> List[List[cp.ndarray]]:
+        return self.__dervatives_signals_batches_list
+    
+    @orthonormalized_dS_dtheta_batches_list.setter
+    def orthonormalized_dS_dtheta_batches_list(self, new_value)-> None:
+        self.__dervatives_signals_batches_list = new_value
+
+    @property
+    def error_e(self)-> cp.ndarray:
+        return self.__error_e
+    
+    @error_e.setter
+    def error_e(self, new_value)-> None:
+        self.__error_e = new_value
+
+    @property
+    def error_de_dtheta_list(self)-> List[cp.ndarray]:
+        return self.__error_de_dtheta_list
+    
+    @error_de_dtheta_list.setter
+    def error_de_dtheta_list(self, new_value)-> None:
+        self.__error_de_dtheta_list = new_value
+
+    

gem/analysis/prf_r2_variance_explain.py

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+import numpy as np
+import cupy as cp
+from gem.tools.json_file_operations import JsonMgr
+from gem.utils.hpc_cupy_utils import HpcUtils as Utils
+from gem.model import prf_model
+from gem.signals.signal_synthesizer import SignalSynthesizer
+from gem.model.prf_model import GaussianModelParams
+from gem.utils.gem_gpu_manager import GemGpuManager as ggm
+
+class R2:
+    @classmethod
+    def get_r2_new_method_with_epsilon_as_Fx(cls, Y_signals_gpu, O_gpu, epsilon_results_cpu):    
+        r2 = []
+        R_Rt_gpu = cp.eye(O_gpu.shape[0]) - O_gpu
+
+        num_y_signals = len(epsilon_results_cpu)
+        for yIdx in range (num_y_signals):
+            y = Y_signals_gpu[:, yIdx]
+            yty = y.T @ y
+            ystar = O_gpu @ y
+            ystarT_ystar_inv = (ystar.T @ ystar) ** (-1)            
+            e = (float(epsilon_results_cpu[yIdx])) ** 2 #<----------------------------------
+            yt_RRt_y = (y.T @ R_Rt_gpu) @ y
+            r2_gpu = 1 - ((yty - e - yt_RRt_y) * ystarT_ystar_inv)
+            r2.append(float(r2_gpu))
+
+        return r2   
+
+    @classmethod
+    def get_r2_num_den_method_with_epsilon_as_yTs(cls, Y_signals_gpu, O_gpu, refined_matching_results, refined_S_cpu):  
+        with cp.cuda.Device(ggm.get_instance().default_gpu_id):  
+            numerators_gpu , denominators_gpu = cls.get_r2_numerator_denominator_terms(Y_signals_gpu, O_gpu, refined_matching_results, refined_S_cpu)
+            r2_results_gpu = 1 - (numerators_gpu / denominators_gpu)
+
+            return cp.asnumpy(r2_results_gpu)   
+
+    @classmethod # R2 numerator = (yty - e - yt_RRt_y)    
+    def get_r2_numerator_denominator_terms(cls, Y_signals_gpu, O_gpu, refined_matching_results, refined_signals_cpu: np.ndarray): 
+        with cp.cuda.Device(ggm.get_instance().default_gpu_id):
+            refined_signals_gpu = cp.asarray(refined_signals_cpu)
+            num_y_signals = Y_signals_gpu.shape[1]
+
+            R_Rt_gpu = cp.eye(O_gpu.shape[0]) - O_gpu
+
+            # Compute yty for each signal
+            yty = cp.sum(Y_signals_gpu ** 2, axis=0)
+
+            # Compute ystar and ystarT_ystar
+            ystar = O_gpu @ Y_signals_gpu
+            ystarT_ystar = cp.sum(ystar ** 2, axis=0)
+
+            # Check for NaN refined results
+            nan_mask = np.isnan(refined_matching_results).all(axis=1)
+            nan_mask = cp.asarray(nan_mask)
+
+            # Check for zero signals
+            s = refined_signals_gpu
+            zero_mask = np.all(refined_signals_cpu == 0, axis=1)
+            zero_mask = cp.asarray(zero_mask)
+
+            # Compute s_star
+            s_star = O_gpu @ s.T  # shape: [timepoints, num_signals]
+
+            # Normalize s_star to get s_prime
+            s_prime = s_star * (cp.sum(s_star ** 2, axis=0) ** (-0.5)) 
+
+            # Compute error-term e = (y.T @ s_prime)^2
+            e = cp.sum(Y_signals_gpu * s_prime, axis=0) ** 2 #<----------------------------------
+
+            # Compute yt_RRt_y
+            # # yt_RRt_y = cp.sum(Y_signals_gpu * (R_Rt_gpu @ Y_signals_gpu), axis=0)
+            yt_R = Y_signals_gpu * (R_Rt_gpu @ Y_signals_gpu)
+            yt_RRt_y = cp.sum(yt_R, axis=0)
+
+            # Compute final numerator and denominator
+            num = yty - e - yt_RRt_y
+            den = ystarT_ystar
+
+            # Apply masks for nan/zero
+            num = cp.where(nan_mask, 2.0, num)
+            num = cp.where(zero_mask & ~nan_mask, 3.0, num)
+            den = cp.where(nan_mask | zero_mask, 1.0, den)
+
+            return num, den
+
+    @classmethod
+    def format_in_json_format(cls, r2_results, refined_matching_results, refined_signal_timecourses, refined_signals_present = True):
+        json_data_results_with_r2 = []
+
+        # default r2 value
+        for i in range((len(refined_matching_results))):
+            r2 = float(r2_results[i])            
+            muX, muY, sigma = refined_matching_results[i]    
+            if refined_signals_present:
+                refined_signal_timecourse = refined_signal_timecourses[i]
+            else:        
+                refined_signal_timecourse = np.array([None])
+            json_entry = JsonMgr.args2jsonEntry(muX, muY, sigma, r2, refined_signal_timecourse)    
+            json_data_results_with_r2.append(json_entry)    
+
+        return json_data_results_with_r2   

gem/configs/__init__.py

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+class my_class(object):
+    pass
+
+
+
+

gem/configs/analysis_configs/analysis_config.xml

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+<!-- XML representation of JSON data -->
+<!-- 
+    "@Author  :   Siddharth Mittal",
+    "@Version :   1.0",
+    "@Contact :   siddharth.mittal@meduniwien.ac.at",
+    "@License :   (C)Copyright 2024, Medical University of Vienna"
+-->
+
+<!-- NOTE for Analysis: For DUMMY/Analsis, set correct Visual field at two positions, one for the <stimulus> and another for <search_space>-->
+
+
+<root>
+  <!-- Path information -->
+  <path_to_append>.../</path_to_append>
+  <refine_fitting enable="True" refinefit_on_gpu="True"/> <!-- Execute refine fitting on GPU if sufficient GPU memory is available -->
+
+  <!-- Stimulus data -->
+  <stimulus>
+    <!-- File path for stimulus -->
+    <directory>/ceph/mri.meduniwien.ac.at/projects/physics/fmri/data/stimsim24/BIDS/derivatives/prfprepare/analysis-01/sub-001/stimuli</directory>    
+    <visual_field>9</visual_field> <!-- Visual field Radius, NOTE: Use "10" for simulated data, else "9" -->
+    <width>101</width>
+    <height>101</height>
+    <binarization enable="False" threshold="0"/> <!-- stimulus will be binarized if enabled, all values above threshold will be set to 1 and below to 0 -->	
+    
+    <!-- Compute model signals with high-res stimulus then downsample: "num_frames_downsampled" = your fMRI timecourse length, "slice_time_ref" for details see https://www.alivelearn.net/?p=1037 -->
+    <high_temporal_resolution enable="false" num_frames_downsampled="240" slice_time_ref="0.5"/>
+  </stimulus>
+
+  <!-- Input Data -->
+  <input_datasrc>    
+    <BIDS enable="True" run_type="individual"> <!-- Set to "True" if the input data is organized in BIDS format, select "individual" or "concatenated" run type -->
+      <basepath>/ceph/mri.meduniwien.ac.at/projects/physics/fmri/data/stimsim24/BIDS</basepath>
+      <append_to_basepath>derivatives, prfprepare</append_to_basepath> <!-- specify if the "analysis-xx"  -->          
+      <!-- <basepath>D:/results/fmri/generic/</basepath>           -->
+
+      <!-- Directory name for results; backups created with timestamp if overwrite="True" -->
+      <results_anaylsis_id overwrite="False">GEMpRF</results_anaylsis_id>
+            
+      <!-- 
+        NOTE: Case sensitive, provide the exact values!!!
+        For the analysis, sub, ses, task, run, hemi,
+        either provide comma separated values or specify "all" (to go through every available analysis) 
+        Sample: <analysis>01, 02</analysis> or <analysis>all</analysis>
+      -->
+      <analysis>01</analysis>
+      <sub>001, 002</sub>
+      <hemi>all</hemi>
+
+      <!--INDIVIDUAL Task/stimulus Analysis-->
+      <individual>
+        <task>bar</task> <!--name of the stimulus, this will be used to find the file in the stimulus directory, ONLY one value is allowed-->  
+        <ses>001nn</ses> <!-- comma separated values or specify "all" -->        
+        <run>01, 02</run> <!-- comma separated values or specify "all" -->
+      </individual>
+
+      <!--CONCATENATED Analysis-->
+      <concatenated>
+        <concatenate_item>
+          <ses>001</ses> <!-- ONLY one value is allowed-->
+          <task>bar</task> <!-- ONLY one value is allowed-->
+          <run>02</run> <!-- ONLY one value is allowed-->
+        </concatenate_item>
+        <concatenate_item>
+          <ses>001</ses>
+          <task>bar</task>
+          <run>04</run>
+        </concatenate_item>
+      </concatenated>       
+    </BIDS>
+
+    <!--OR, make Bids False and specify directly single/multiple filepaths -->
+    <fixed_paths>
+      <measured_data_filepath> <!-- Measured input data filepaths -->
+        <filepath>/ceph/mri.meduniwien.ac.at/projects/physics/fmri/data/tests/gem_generic_test/BIDS/sub-001/ses-3n2/func/sub-001_ses-3n2_task-prf_acq-normal_run-01_bold.nii.gz</filepath>
+        <filepath>dummy////sub-001/ses-3n2/func/sub-001_ses-3n2_task-prf_acq-normal_run-01_bold.nii.gz</filepath>
+      </measured_data_filepath>              
+      <results> <!-- Results filepaths realted  -->
+        <basepath>/ceph/mri.meduniwien.ac.at/projects/physics/fmri/data/tests/gem_generic_test/derivatives/prfanalyze-gem/analysis-01/sub-001/ses-3n2/</basepath> <!-- Base path for results -->    
+        <custom_filename_postfix>_[gem-new_data-simulated_v1_151x151x8_refine-validation]</custom_filename_postfix> <!-- Custom filename postfix -->    
+        <prepend_date>True</prepend_date> <!-- Flag to prepend date -->
+      </results>
+    </fixed_paths>
+  </input_datasrc>
+
+  <!-- Analysis Model -->
+  <pRF_model>    
+    <model>2d_gaussian</model> <!-- 2d_gauss, (DoG, CSS not avaiable at the moment) -->
+  </pRF_model>
+
+  <!-- Measured data section -->
+  <measured_data>
+    <width>101</width>
+    <height>101</height>
+    <batches>200</batches>    
+  </measured_data>
+
+  <!-- GPU configuration -->
+  <gpu>
+    <!-- Default GPU -->
+    <default_gpu>0</default_gpu>
+    <!-- Additional available GPUs -->
+    <additional_available_gpus>
+      <gpu>1</gpu>
+      <gpu>2</gpu>
+      <gpu>3</gpu>
+    </additional_available_gpus>
+  </gpu>
+
+  <!-- Search space information -->
+  <search_space write_debug_info="false">    
+    <!-- if the user wants to use custom HRF, pRF sizes or Spatial grid, provide the filepath to the H5 file and the keys for each parameter -->
+    <optional_analysis_params enable="False" filepath="DIR_PATH/analysis_additional_params.h5">
+      <hrf use_from_file="True" key="analysis_params/hrf_values"/>
+      <sigmas use_from_file="True" key="analysis_params/sigmas"/>
+      <spatial_grid_xy use_from_file="True" key="analysis_params/spatial_grid_xy"/>
+    </optional_analysis_params>
+    
+    <!-- if the user wants to generate a rectilinear grid within the GEM-pRF program, specify the default values below. Please NOTE that these values will ONLY be used if their corresponding optional_analysis_params = False -->
+    <default_hrf t="(0, 45)" TR="auto" peak_delay="6.16" under_shoot_delay="12.0" peak_disp="0.85" under_disp="0.82" peak_to_undershoot="2.15" normalize="true"/> <!-- SPM parameters, "t" is fed to np.arange(start, stop, step), "step" represents the TR value, set it to a lower value in case of high temporal stimulus. If TR = "auto" then, its value will be read from the stimulus file -->
+    <default_spatial_grid visual_field_radius="13.5" num_horizontal_prfs="151" num_vertical_prfs="151"/>
+    <default_sigmas num_sigmas="16" min_sigma="0.5" max_sigma="5"/>
+  </search_space>
+</root>

gem/configs/config_manager.py

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+# -*- coding: utf-8 -*-
+"""
+"@Author  :   Siddharth Mittal",
+"@Version :   1.0",
+"@Contact :   siddharth.mittal@meduniwien.ac.at",
+"@License :   (C)Copyright 2023-2025, Medical University of Vienna",
+"@Desc    :   None",
+
+"""
+
+import json
+import os
+from enum import Enum
+import xmltodict
+
+class RunType(Enum):
+    ANALYSIS = 1
+    SIMULATION = 2
+
+class ConfigurationWrapper:
+    config_data = None
+
+    @classmethod
+    def __read_xml_file(cls, run_type: RunType = None, config_filepath : str = None):
+        script_dir = os.path.dirname(os.path.realpath(__file__))  # Get the directory of the script
+        
+        if config_filepath is not None:
+            config_file_path = config_filepath
+        else:
+             config_file_path = os.path.join(script_dir, "default_config", "default_config.xml") # default config file path
+
+        if os.path.isfile(config_file_path):
+            with open(config_file_path) as xml_file:            
+                config_data_dict = xmltodict.parse(xml_file.read())
+                xml_file.close()            
+
+                 # XML to JSON data conversion
+                str_config_data = json.dumps(config_data_dict)
+                json_config_data = json.loads(str_config_data)
+                cls.config_data = json_config_data.get("root")
+        else:
+            print("Config file not found. Make sure it's located in the same directory as the script.")    
+
+    @classmethod
+    def parse_attrs(cls, node, types=None):
+        """Extracts attributes (removes '@'), converts values using types dict if provided."""
+        if node is None:
+            return {}
+        types = types or {}
+        return {
+            k.lstrip("@"): types.get(k.lstrip("@"), str)(v)
+            for k, v in node.items()
+            if k.startswith("@")
+        }  
+
+    @classmethod
+    def load_configuration(cls, run_type: RunType = None, config_filepath : str = None):
+        # if cls.config_data is None: #NOTE: This sometimes lead to unpredictable results, to be on safe side, always load the configuration
+        cls.__read_xml_file(run_type, config_filepath) 
+            # # cls._read_json_file(run_type)
+
+        # path_to_append
+        cls.path_to_append = cls.config_data.get("path_to_append")
+
+        # Input data source
+        # ...BIDS
+        cls.bids = (cls.config_data.get("input_datasrc")).get("BIDS") # sample: {'@enable': 'True', 'basepath': 'D:/results/fmri/generic/', 'analysis': None, 'sub': None, 'ses': None}
+        # ...Non-BIDS i.e. direct filepaths
+        cls.fixed_paths = (cls.config_data.get("input_datasrc")).get("fixed_paths")
+
+        # result_file_path
+        cls.result_file_path = cls.config_data.get("result_file_path")        
+
+        # results
+        #cls.results = cls.config_data.get("results")
+        cls.results = (cls.config_data.get("input_datasrc")).get("fixed_paths").get("results")
+
+        # PRF Model
+        cls.pRF_model_details = cls.config_data.get("pRF_model")
+
+        # Stimulus
+        cls.stimulus = cls.config_data.get("stimulus")
+        # ...subnodes of stimulus
+        high_temp_res_node = cls.stimulus.get("high_temporal_resolution", {})
+        cls.stimulus_high_temporal_resolution = cls.parse_attrs(high_temp_res_node, {
+            "enable": lambda v: v.lower() == "true",
+            "num_frames_downsampled": int,
+            "slice_time_ref": float
+        })
+        
+        # Measure Data
+        cls.measured_data = cls.config_data.get("measured_data")
+        
+        # Search Space
+        cls.search_space = cls.config_data.get("search_space")
+
+        # ...whether to write debug info or not
+        search_space_attrs = cls.parse_attrs(cls.search_space, {
+            "write_debug_info": lambda v: v.lower() == "true"
+        })
+        cls.write_debug_info = search_space_attrs.get("write_debug_info", False)  
+
+        # Concatenated runs
+        cls.concatenated_runs = cls.config_data.get("concatenated_runs")        
+
+        # Test Space
+        cls.test_space = cls.config_data.get("test_space")
+
+        # Noise
+        cls.noise = cls.config_data.get("noise")           
+
+        # GPU
+        cls.gpu = cls.config_data.get("gpu")           
+
+        # Enable/disable Refine fitting  
+        refine_fitting_node_params = cls.parse_attrs(cls.config_data.get("refine_fitting", {}), {
+            "enable": lambda v: v.lower() == "true",
+            "refinefit_on_gpu": lambda v: v.lower() == "true"
+        })
+        cls.refine_fitting_enabled = refine_fitting_node_params['enable']
+        cls.is_refinefit_on_gpu = refine_fitting_node_params['refinefit_on_gpu']
+     
+        # Optional analysis params
+        opt_node = cls.search_space.get("optional_analysis_params", {})
+        cls.optional_analysis_params = cls.parse_attrs(opt_node, {
+            "enable": lambda v: v.lower() == "true",
+            "filepath": str
+        })
+
+        # ...subnodes of optional_analysis_params
+        for key in ["hrf", "sigmas", "spatial_grid_xy"]:
+            subnode = opt_node.get(key, {})  # <--- get from original XML dict
+            cls.optional_analysis_params[key] = cls.parse_attrs(subnode, {
+                "use_from_file": lambda v: v.lower() == "true",
+                "key": str
+            })   
+
+        # default spatial grid
+        cls.default_spatial_grid = cls.parse_attrs(cls.search_space.get("default_spatial_grid"), {
+            "visual_field_radius": float,
+            "num_horizontal_prfs": int,
+            "num_vertical_prfs": int
+        })
+
+        # default sigmas
+        cls.default_sigmas = cls.parse_attrs(cls.search_space.get("default_sigmas"), {
+            "num_sigmas": int,
+            "min_sigma": float,
+            "max_sigma": float
+        })
+
+        # default hrf
+        cls.default_hrf = cls.parse_attrs(cls.search_space.get("default_hrf"), {
+            "t": lambda v: tuple(map(float, v.strip("()").split(","))),  # expects a string like "(0, 45)"
+            "TR": lambda v: float(v) if v.replace('.', '', 1).isdigit() else None,
+            "peak_delay": float,
+            "under_shoot_delay": float,
+            "peak_disp": float,
+            "under_disp": float,
+            "peak_to_undershoot": float,
+            "normalize": lambda v: v.lower() == "true"
+        })
+
+        print("Successfully read the config file. ")
+        if cls.optional_analysis_params['enable']:
+            print(f"Analysis params from file: {', '.join(k for k,v in cls.optional_analysis_params.items() if isinstance(v, dict) and v.get('use_from_file', False)) or 'None'}")
+
+# Usage:
+if __name__ == "__main__":
+    ConfigurationWrapper.load_configuration(RunType.ANALYSIS)
+
+    # Access the configuration parameters using the class itself
+    print(f"Visual Field Size: {ConfigurationWrapper.path_to_appended}")
+    print(f"Stimulus: {ConfigurationWrapper.stimulus}")

gem/configs/default_config/default_config - old before concatenation.xml

@@ -0,0 +1,141 @@
+<!-- XML representation of JSON data -->
+<!-- 
+    "@Author  :   Siddharth Mittal",
+    "@Version :   1.0",
+    "@Contact :   siddharth.mittal@meduniwien.ac.at",
+    "@License :   (C)Copyright 2024, Medical University of Vienna"
+-->
+
+<!-- NOTE for Analysis: For DUMMY/Analsis, set correct Visual field at two positions, one for the <stimulus> and another for <search_space>-->
+
+
+<root>
+  <!-- Path information -->
+  <path_to_append>/ceph/mri.meduniwien.ac.at/departments/physics/fmrilab/home/smittal/dgx-versions/fmri/</path_to_append>
+
+  <!-- Input Data -->
+  <input_datasrc>    
+    <!-- either spcify the BIDS info and set enable=True -->  
+    <BIDS enable="False"> <!-- Flag to indicate BIDS format -->
+      <basepath>D:/results/gem-paper-simulated-data/analysis/08/BIDS/</basepath>
+      <append_to_basepath>derivatives, prfsynth</append_to_basepath> <!-- specify if the "analysis-xx"  -->          
+      <!-- <basepath>D:/results/fmri/generic/</basepath>           -->
+
+      <!-- 
+        NOTE: Case sensitive, provide the exact values!!!
+        For the analysis, sub, ses, task, run, hemi,
+        either provide comma separated values or specify "all" (to go through every available analysis) 
+        Sample: <analysis>01, 02</analysis> or <analysis>all</analysis>
+      -->
+      <analysis>08</analysis> 
+      <sub>HighNoise</sub> 
+      <ses>0n0, 3n3, 6n6</ses>
+      <task>prf</task> 
+      <run>all</run>
+      <hemi>all</hemi>
+      <results_anaylsis_id>01</results_anaylsis_id> <!-- analysis id to save the results -->
+    </BIDS>
+
+    <!--OR, make Bids False and specify directly single/multiple filepaths -->
+    <fixed_paths>
+      <measured_data_filepath> <!-- Measured input data filepaths -->
+        <filepath>Y:\data\tests\gem-paper-simulated-data\analysis\04\BIDS\derivatives\prfsynth\analysis-04\sub-001\ses-3n2\func\sub-001_ses-3n2_task-prf_acq-normal_run-01_bold.nii.gz</filepath>
+        <filepath>...dummy_filepath.....</filepath>
+      </measured_data_filepath>              
+      <results> <!-- Results filepaths realted  -->
+        <basepath>D:\results\fmri/generic/</basepath> <!-- Base path for results -->
+        <custom_filename_postfix>_[gem-benchmark_51x51x8]</custom_filename_postfix> <!-- Custom filename postfix -->    
+        <prepend_date>True</prepend_date> <!-- Flag to prepend date -->
+      </results>
+    </fixed_paths>
+  </input_datasrc>
+
+  <!-- Analysis Model -->
+  <pRF_model_details>    
+    <model>2d_gaussian</model> <!-- 2d_gauss, DoG, CSS -->
+  </pRF_model_details>
+
+
+
+  <!-- Stimulus data -->
+  <stimulus>
+    <!-- File path for stimulus -->
+    <filepath>Y:\data\tests\gem-paper-simulated-data\analysis\04\BIDS\stimuli\sub-001_ses-3n2_task-prf_apertures.nii.gz</filepath>
+    <visual_field>10</visual_field> <!-- Visual field Radius, NOTE: Use "10" for simulated data, else "9" -->
+    <width>101</width>
+    <height>101</height>
+  </stimulus>
+
+  <!-- Measured data section -->
+  <measured_data>
+    <width>101</width>
+    <height>101</height>
+    <batches>16</batches>    
+  </measured_data>
+
+  <!-- GPU configuration -->
+  <gpu>
+    <!-- Default GPU -->
+    <default_gpu>0</default_gpu>
+    <!-- Additional available GPUs -->
+    <additional_available_gpus>
+      <gpu>0</gpu>
+      <gpu>1</gpu>
+      <gpu>3</gpu>
+    </additional_available_gpus>
+  </gpu>
+
+  <!-- Search space information -->
+  <search_space>    
+    <visual_field>13.5</visual_field> <!-- NOTE: use "9" for analysis with DUMMY signal because the signal is generated using maxEcc=9 ....and the visual field is 13.5 degrees for NORMAL analysis.-->
+    <nRows>51</nRows>
+    <nCols>51</nCols>
+    <min_sigma>0.5</min_sigma>
+    <max_sigma>5</max_sigma>
+    <nSigma>8</nSigma>
+  </search_space>
+
+  <!-- Test space information -->
+  <test_space>
+    <nRows>11</nRows>
+    <nCols>11</nCols>
+    <min_sigma>0.5</min_sigma>
+    <max_sigma>4</max_sigma>
+    <nSigma>1</nSigma>
+  </test_space>
+
+  <!-- Concatenated runs information -->
+  <concatenated_runs>
+    <enable>True</enable>
+    <num_runs>2</num_runs>
+    <height>101</height>
+    <batches>4</batches>
+    
+    <!-- BIDS run information -->
+    <bids_runs>
+      <run>01</run>
+      <run>02</run>
+    </bids_runs>
+    <!-- BIDS task information -->
+    <bids_tasks>
+      <task>bar</task>
+      <task>ring</task>
+    </bids_tasks>
+    <!-- Stimulus file paths -->
+    <stimulus>
+      <filepath>/ceph/mri.meduniwien.ac.at/projects/physics/fmri/data/stimsim23/derivatives/prfprepare/analysis-03/sub-sidtest/stimuli/task-bar_apertures.nii.gz</filepath>
+      <filepath>/ceph/mri.meduniwien.ac.at/projects/physics/fmri/data/stimsim23/derivatives/prfprepare/analysis-03/sub-sidtest/stimuli/task-bar_apertures.nii.gz</filepath>
+    </stimulus>
+    <!-- Measured data file paths -->
+    <measured_data>
+      <filepath>/ceph/mri.meduniwien.ac.at/projects/physics/fmri/data/stimsim23/derivatives/prfprepare/analysis-03/sub-sidtest/ses-001/func/sub-sidtest_ses-001_task-bar_run-01_hemi-L_bold.nii.gz</filepath>
+    </measured_data>
+  </concatenated_runs>
+
+  <!-- Noise information -->
+  <noise>    
+    <level>0.1</level>    
+    <model>gaussian</model>    
+    <synthesis_ratio>1</synthesis_ratio> <!-- number of noisy signals per pRF location -->
+  </noise>
+</root>