#include <SPI.h>
#include <SD.h>

File myFile;

struct s1 {
  uint16_t v16;
  uint32_t v32;
};
s1 structvar;

struct s2 {
  uint16_t v16_1;
  uint16_t v16_2;
  uint16_t v16_3;
};
s2 structvar2;

uint16_t v16;
uint32_t v32;

void setup() {
  Serial.begin(9600);

  Serial.print("Initializing SD card...");

  if (!SD.begin(4)) {
    Serial.println("initialization failed!");
    return;
  }
  Serial.println("initialization done.");

  myFile = SD.open("IMAGE001.BMP", FILE_READ);
  if (myFile) {
    Serial.println("Struct1");
    myFile.read(&structvar,6);
    Serial.println(structvar.v16);
    Serial.println(structvar.v32);

    myFile.seek(0);
    Serial.println("Struct2");
    myFile.read(&structvar2,6);
    Serial.println(structvar2.v16_1);
    Serial.println(structvar2.v16_2);
    Serial.println(structvar2.v16_3);

    myFile.seek(0);
    Serial.println("Separate vars");
    myFile.read(&v16,2);
    myFile.read(&v32,4);
    Serial.println(v16);
    Serial.println(v32);

    myFile.close();
  }
}

void loop() {
  // nothing happens after setup finishes.
  delay(100);
}

Struct1
19778    //0x4d42
1        //0x00000001 - Lower half only
4        //4 Bytes - correct size.

Struct2
19778    //0x4d42
58934    //0xe636 - Upper Half
1        //0x0001 - Lower Half

Separate vars
19778    //0x4d42
124470   //0x0001e636 - Correct