STM32 Nucleo-F446RE Encoder Count only printing 0

I am trying to read the output of an encoder using CubeIDE. I have a DC motor with a magnetic encoder attached. When the encoders are measured using a multi-meter the outputs are ranging between 0 to 5V when rotating. But when connected to the Nucleo through a timer's encoder mode, the output is printing as 0. I have tried multiple timers and have verified the connection.

This is my current set up. What is wrong with my code/set up?

/* Includes ------------------------------------------------------------------*/
#include "main.h"

/* Private includes ----------------------------------------------------------*/
/* USER CODE BEGIN Includes */
#include <stdio.h>
#include <string.h>
/* USER CODE END Includes */

/* Private variables ---------------------------------------------------------*/
TIM_HandleTypeDef htim3;

UART_HandleTypeDef huart2;

/* USER CODE BEGIN PV */
volatile int16_t encoder_count = 0;
char msg[30];
/* USER CODE END PV */

/* Private function prototypes -----------------------------------------------*/
void SystemClock_Config(void);
static void MX_GPIO_Init(void);
static void MX_USART2_UART_Init(void);
static void MX_TIM3_Init(void);
/* USER CODE BEGIN PFP */

/* USER CODE END PFP */

/* Private user code ---------------------------------------------------------*/
/* USER CODE BEGIN 0 */

/* USER CODE END 0 */

/**
  * @brief  The application entry point.
  * @retval int
  */
int main(void)
{

  /* USER CODE BEGIN 1 */

  /* USER CODE END 1 */

  /* MCU Configuration--------------------------------------------------------*/

  /* Reset of all peripherals, Initializes the Flash interface and the Systick. */
  HAL_Init();

  /* USER CODE BEGIN Init */

  /* USER CODE END Init */

  /* Configure the system clock */
  SystemClock_Config();

  /* USER CODE BEGIN SysInit */
  HAL_TIM_Encoder_Start(&htim3, TIM_CHANNEL_ALL);
  /* USER CODE END SysInit */

  /* Initialize all configured peripherals */
  MX_GPIO_Init();
  MX_USART2_UART_Init();
  MX_TIM3_Init();
  /* USER CODE BEGIN 2 */

  /* USER CODE END 2 */

  /* Infinite loop */
  /* USER CODE BEGIN WHILE */
  while (1)
  {
      encoder_count =  __HAL_TIM_GET_COUNTER(&htim3);
      snprintf(msg, sizeof(msg), "Encoder count: %d\r\n", encoder_count);
      HAL_UART_Transmit(&huart2, (uint8_t*)msg, strlen(msg), HAL_MAX_DELAY);
      HAL_Delay(500);
    /* USER CODE END WHILE */

    /* USER CODE BEGIN 3 */
  }
  /* USER CODE END 3 */
}

/**
  * @brief System Clock Configuration
  * @retval None
  */
void SystemClock_Config(void)
{
  RCC_OscInitTypeDef RCC_OscInitStruct = {0};
  RCC_ClkInitTypeDef RCC_ClkInitStruct = {0};

  /** Configure the main internal regulator output voltage
  */
  __HAL_RCC_PWR_CLK_ENABLE();
  __HAL_PWR_VOLTAGESCALING_CONFIG(PWR_REGULATOR_VOLTAGE_SCALE3);

  /** Initializes the RCC Oscillators according to the specified parameters
  * in the RCC_OscInitTypeDef structure.
  */
  RCC_OscInitStruct.OscillatorType = RCC_OSCILLATORTYPE_HSE;
  RCC_OscInitStruct.HSEState = RCC_HSE_ON;
  RCC_OscInitStruct.PLL.PLLState = RCC_PLL_ON;
  RCC_OscInitStruct.PLL.PLLSource = RCC_PLLSOURCE_HSE;
  RCC_OscInitStruct.PLL.PLLM = 4;
  RCC_OscInitStruct.PLL.PLLN = 90;
  RCC_OscInitStruct.PLL.PLLP = RCC_PLLP_DIV4;
  RCC_OscInitStruct.PLL.PLLQ = 2;
  RCC_OscInitStruct.PLL.PLLR = 2;
  if (HAL_RCC_OscConfig(&RCC_OscInitStruct) != HAL_OK)
  {
    Error_Handler();
  }

  /** Initializes the CPU, AHB and APB buses clocks
  */
  RCC_ClkInitStruct.ClockType = RCC_CLOCKTYPE_HCLK|RCC_CLOCKTYPE_SYSCLK
                              |RCC_CLOCKTYPE_PCLK1|RCC_CLOCKTYPE_PCLK2;
  RCC_ClkInitStruct.SYSCLKSource = RCC_SYSCLKSOURCE_PLLRCLK;
  RCC_ClkInitStruct.AHBCLKDivider = RCC_SYSCLK_DIV1;
  RCC_ClkInitStruct.APB1CLKDivider = RCC_HCLK_DIV2;
  RCC_ClkInitStruct.APB2CLKDivider = RCC_HCLK_DIV1;

  if (HAL_RCC_ClockConfig(&RCC_ClkInitStruct, FLASH_LATENCY_2) != HAL_OK)
  {
    Error_Handler();
  }
}

/**
  * @brief TIM3 Initialization Function
  * @param None
  * @retval None
  */
static void MX_TIM3_Init(void)
{

  /* USER CODE BEGIN TIM3_Init 0 */

  /* USER CODE END TIM3_Init 0 */

  TIM_Encoder_InitTypeDef sConfig = {0};
  TIM_MasterConfigTypeDef sMasterConfig = {0};

  /* USER CODE BEGIN TIM3_Init 1 */

  /* USER CODE END TIM3_Init 1 */
  htim3.Instance = TIM3;
  htim3.Init.Prescaler = 0;
  htim3.Init.CounterMode = TIM_COUNTERMODE_UP;
  htim3.Init.Period = 65535;
  htim3.Init.ClockDivision = TIM_CLOCKDIVISION_DIV1;
  htim3.Init.AutoReloadPreload = TIM_AUTORELOAD_PRELOAD_DISABLE;
  sConfig.EncoderMode = TIM_ENCODERMODE_TI12;
  sConfig.IC1Polarity = TIM_ICPOLARITY_RISING;
  sConfig.IC1Selection = TIM_ICSELECTION_DIRECTTI;
  sConfig.IC1Prescaler = TIM_ICPSC_DIV1;
  sConfig.IC1Filter = 0;
  sConfig.IC2Polarity = TIM_ICPOLARITY_RISING;
  sConfig.IC2Selection = TIM_ICSELECTION_DIRECTTI;
  sConfig.IC2Prescaler = TIM_ICPSC_DIV1;
  sConfig.IC2Filter = 0;
  if (HAL_TIM_Encoder_Init(&htim3, &sConfig) != HAL_OK)
  {
    Error_Handler();
  }
  sMasterConfig.MasterOutputTrigger = TIM_TRGO_RESET;
  sMasterConfig.MasterSlaveMode = TIM_MASTERSLAVEMODE_DISABLE;
  if (HAL_TIMEx_MasterConfigSynchronization(&htim3, &sMasterConfig) != HAL_OK)
  {
    Error_Handler();
  }
  /* USER CODE BEGIN TIM3_Init 2 */

  /* USER CODE END TIM3_Init 2 */

}

/**
  * @brief USART2 Initialization Function
  * @param None
  * @retval None
  */
static void MX_USART2_UART_Init(void)
{

  /* USER CODE BEGIN USART2_Init 0 */

  /* USER CODE END USART2_Init 0 */

  /* USER CODE BEGIN USART2_Init 1 */

  /* USER CODE END USART2_Init 1 */
  huart2.Instance = USART2;
  huart2.Init.BaudRate = 115200;
  huart2.Init.WordLength = UART_WORDLENGTH_8B;
  huart2.Init.StopBits = UART_STOPBITS_1;
  huart2.Init.Parity = UART_PARITY_NONE;
  huart2.Init.Mode = UART_MODE_TX_RX;
  huart2.Init.HwFlowCtl = UART_HWCONTROL_NONE;
  huart2.Init.OverSampling = UART_OVERSAMPLING_16;
  if (HAL_UART_Init(&huart2) != HAL_OK)
  {
    Error_Handler();
  }
  /* USER CODE BEGIN USART2_Init 2 */

  /* USER CODE END USART2_Init 2 */

}

/**
  * @brief GPIO Initialization Function
  * @param None
  * @retval None
  */
static void MX_GPIO_Init(void)
{
  GPIO_InitTypeDef GPIO_InitStruct = {0};
/* USER CODE BEGIN MX_GPIO_Init_1 */
/* USER CODE END MX_GPIO_Init_1 */

  /* GPIO Ports Clock Enable */
  __HAL_RCC_GPIOC_CLK_ENABLE();
  __HAL_RCC_GPIOH_CLK_ENABLE();
  __HAL_RCC_GPIOA_CLK_ENABLE();
  __HAL_RCC_GPIOB_CLK_ENABLE();

  /*Configure GPIO pin Output Level */
  HAL_GPIO_WritePin(LD2_GPIO_Port, LD2_Pin, GPIO_PIN_RESET);

  /*Configure GPIO pin : B1_Pin */
  GPIO_InitStruct.Pin = B1_Pin;
  GPIO_InitStruct.Mode = GPIO_MODE_IT_FALLING;
  GPIO_InitStruct.Pull = GPIO_NOPULL;
  HAL_GPIO_Init(B1_GPIO_Port, &GPIO_InitStruct);

  /*Configure GPIO pin : LD2_Pin */
  GPIO_InitStruct.Pin = LD2_Pin;
  GPIO_InitStruct.Mode = GPIO_MODE_OUTPUT_PP;
  GPIO_InitStruct.Pull = GPIO_NOPULL;
  GPIO_InitStruct.Speed = GPIO_SPEED_FREQ_LOW;
  HAL_GPIO_Init(LD2_GPIO_Port, &GPIO_InitStruct);

/* USER CODE BEGIN MX_GPIO_Init_2 */
/* USER CODE END MX_GPIO_Init_2 */
}

/* USER CODE BEGIN 4 */

/* USER CODE END 4 */

/**
  * @brief  This function is executed in case of error occurrence.
  * @retval None
  */
void Error_Handler(void)
{
  /* USER CODE BEGIN Error_Handler_Debug */
  /* User can add his own implementation to report the HAL error return state */
  __disable_irq();
  while (1)
  {
  }
  /* USER CODE END Error_Handler_Debug */
}

#ifdef  USE_FULL_ASSERT
/**
  * @brief  Reports the name of the source file and the source line number
  *         where the assert_param error has occurred.
  * @param  file: pointer to the source file name
  * @param  line: assert_param error line source number
  * @retval None
  */
void assert_failed(uint8_t *file, uint32_t line)
{
  /* USER CODE BEGIN 6 */
  /* User can add his own implementation to report the file name and line number,
     ex: printf("Wrong parameters value: file %s on line %d\r\n", file, line) */
  /* USER CODE END 6 */
}
#endif /* USE_FULL_ASSERT */

I have tried multiple different connections, timers and approaches to finding the encoder value. I am wanting to read an accurate encoder value.