Ad5933 analog front end - 4 electrode measuring

It is had to suggest much without seeing the exact schematic with all connections and component values. Referring to a general sketch in your link, first suspect to check would be the DC working point for the entire schematic as the AD5933, generally speaking, requires the AC signals to have zero line at Vdd/2 = 2.5V in your case. Can you check if the DC voltage is 2.5V at:
1. The left pin of Rcurrent resistor
2. The output of the Vref Generator
3. The right pin of Rprotect
4. The left pin of Rin
5. The RF pin of the AD5933
?
If all is well, can you check that the AC voltage at the RFB pin of the AD5933 is a well-formed sinewave without any distortion or clipping at 0V or Vdd or both?
Also, what settings are you programming into the AD5933? Excitation voltage, PGA gain, frequency range, number of settling cycles, etc.? 

Hey  Snorlax, Thanks for your reply!

Im attaching an image of the schematics to make it more clear.

regarding your questions, I have checked for vdc of 2.5v at all the points you suggested and it is indeed 2.5v.

I do see some kind of clipping at the rfb pib and I cant seem to understand why it happens. it clips the lower part of the wave.

 my settings:

supply voltage 5v

Excitation voltage: 2.24v dc offset with vpp of 3v

PGA gain=1

frequency range 50Khz-52Khz

default number of settling cycles 

and if I may, I'd like to add the Arduino code for the full picture:

/*
ad5933-test
    Reads impedance values from the AD5933 over I2C and prints them serially.
*/

#include <Wire.h>
#include "AD5933.h"

#define START_FREQ  (50000)
#define FREQ_INCR   (100)
#define NUM_INCR    (20)
#define REF_RESIST  (1000)

double gain[NUM_INCR+1];
int phase[NUM_INCR+1];

void setup(void)
{
  // Begin I2C
  Wire.begin();

  // Begin serial at 9600 baud for output
  Serial.begin(9600);
  Serial.println("AD5933 Test Started!");

  // Perform initial configuration. Fail if any one of these fail.
  if (!(AD5933::reset() &&
        AD5933::setInternalClock(true) &&
        AD5933::setStartFrequency(START_FREQ) &&
        AD5933::setIncrementFrequency(FREQ_INCR) &&
        AD5933::setNumberIncrements(NUM_INCR) &&
        AD5933::setPGAGain(PGA_GAIN_X1)))
        {
            Serial.println("FAILED in initialization!");
            while (true) ;
        }

  // Perform calibration sweep
  if (AD5933::calibrate(gain, phase, REF_RESIST, NUM_INCR+1))
    Serial.println("Calibrated!");
  else
    Serial.println("Calibration failed...");
}

void loop(void)
{

  // Complex but more robust method for frequency sweep
  frequencySweepRaw();

  // Delay
  delay(5000);
}


void frequencySweepRaw() {
    // Create variables to hold the impedance data and track frequency
    int real, imag, i = 0, cfreq = START_FREQ/1000;

    // Initialize the frequency sweep
    if (!(AD5933::setPowerMode(POWER_STANDBY) &&          // place in standby
          AD5933::setControlMode(CTRL_INIT_START_FREQ) && // init start freq
          AD5933::setControlMode(CTRL_START_FREQ_SWEEP))) // begin frequency sweep
         {
             Serial.println("Could not initialize frequency sweep...");
         }

    // Perform the actual sweep
    while ((AD5933::readStatusRegister() & STATUS_SWEEP_DONE) != STATUS_SWEEP_DONE) {
        // Get the frequency data for this frequency point
        if (!AD5933::getComplexData(&real, &imag)) {
            Serial.println("Could not get raw frequency data...");
        }

        // Print out the frequency data
        Serial.print(cfreq);
        Serial.print(": R=");
        Serial.print(real);
        Serial.print("/I=");
        Serial.print(imag);

        // Compute impedance
        double magnitude = sqrt(pow(real, 2) + pow(imag, 2));
        double impedance = 1/(magnitude*gain[i]);
        Serial.print("  |Z|=");
        Serial.println(impedance);

        // Increment the frequency
        i++;
        cfreq += FREQ_INCR/1000;
        AD5933::setControlMode(CTRL_INCREMENT_FREQ);
    }

    Serial.println("Frequency sweep complete!");

    // Set AD5933 power mode to standby when finished
    if (!AD5933::setPowerMode(POWER_STANDBY))
        Serial.println("Could not set to standby...");
}

I think I have a problem calculating the real gain in the circuit and how to take into account the different resistor values in the final gain calculation.

I would probably also need to incorporate it in the calibration process but since I use a library for the ad5933 I assume I'd have to make my own calibration function?

and if I may, I'd like to add the Arduino code for the full picture:

/*
ad5933-test
    Reads impedance values from the AD5933 over I2C and prints them serially.
*/

#include <Wire.h>
#include "AD5933.h"

#define START_FREQ  (50000)
#define FREQ_INCR   (100)
#define NUM_INCR    (20)
#define REF_RESIST  (1000)

double gain[NUM_INCR+1];
int phase[NUM_INCR+1];

void setup(void)
{
  // Begin I2C
  Wire.begin();

  // Begin serial at 9600 baud for output
  Serial.begin(9600);
  Serial.println("AD5933 Test Started!");

  // Perform initial configuration. Fail if any one of these fail.
  if (!(AD5933::reset() &&
        AD5933::setInternalClock(true) &&
        AD5933::setStartFrequency(START_FREQ) &&
        AD5933::setIncrementFrequency(FREQ_INCR) &&
        AD5933::setNumberIncrements(NUM_INCR) &&
        AD5933::setPGAGain(PGA_GAIN_X1)))
        {
            Serial.println("FAILED in initialization!");
            while (true) ;
        }

  // Perform calibration sweep
  if (AD5933::calibrate(gain, phase, REF_RESIST, NUM_INCR+1))
    Serial.println("Calibrated!");
  else
    Serial.println("Calibration failed...");
}

void loop(void)
{

  // Complex but more robust method for frequency sweep
  frequencySweepRaw();

  // Delay
  delay(5000);
}


void frequencySweepRaw() {
    // Create variables to hold the impedance data and track frequency
    int real, imag, i = 0, cfreq = START_FREQ/1000;

    // Initialize the frequency sweep
    if (!(AD5933::setPowerMode(POWER_STANDBY) &&          // place in standby
          AD5933::setControlMode(CTRL_INIT_START_FREQ) && // init start freq
          AD5933::setControlMode(CTRL_START_FREQ_SWEEP))) // begin frequency sweep
         {
             Serial.println("Could not initialize frequency sweep...");
         }

    // Perform the actual sweep
    while ((AD5933::readStatusRegister() & STATUS_SWEEP_DONE) != STATUS_SWEEP_DONE) {
        // Get the frequency data for this frequency point
        if (!AD5933::getComplexData(&real, &imag)) {
            Serial.println("Could not get raw frequency data...");
        }

        // Print out the frequency data
        Serial.print(cfreq);
        Serial.print(": R=");
        Serial.print(real);
        Serial.print("/I=");
        Serial.print(imag);

        // Compute impedance
        double magnitude = sqrt(pow(real, 2) + pow(imag, 2));
        double impedance = 1/(magnitude*gain[i]);
        Serial.print("  |Z|=");
        Serial.println(impedance);

        // Increment the frequency
        i++;
        cfreq += FREQ_INCR/1000;
        AD5933::setControlMode(CTRL_INCREMENT_FREQ);
    }

    Serial.println("Frequency sweep complete!");

    // Set AD5933 power mode to standby when finished
    if (!AD5933::setPowerMode(POWER_STANDBY))
        Serial.println("Could not set to standby...");
}

I think I have a problem calculating the real gain in the circuit and how to take into account the different resistor values in the final gain calculation.

I would probably also need to incorporate it in the calibration process but since I use a library for the ad5933 I assume I'd have to make my own calibration function?