diff --git a/matlab/EKF_replay/Common/convert_apm_data.m b/matlab/EKF_replay/Common/convert_apm_data.m
index db0b858e74..2b63e2092b 100755
--- a/matlab/EKF_replay/Common/convert_apm_data.m
+++ b/matlab/EKF_replay/Common/convert_apm_data.m
@@ -10,6 +10,7 @@ for source_index = 1:length(BARO)
         output_index = output_index + 1;
     end
 end
+save baro_data.mat baro_data;
 
 %% extract IMU delta angles and velocity data
 clear imu_data;
@@ -18,6 +19,7 @@ imu_data.gyro_dt = IMT(:,5);
 imu_data.del_ang = IMT(:,6:8);
 imu_data.accel_dt = IMT(:,4);
 imu_data.del_vel = IMT(:,9:11);
+save imu_data.mat imu_data;
 
 %% convert magnetomer data
 clear mag_data;
@@ -32,13 +34,17 @@ for source_index = 1:length(MAG)
         output_index = output_index + 1;
     end
 end
+save mag_data.mat mag_data;
 
 %% save GPS daa
 clear gps_data;
-gps_data.time_us = GPS(:,2);
-gps_data.pos_error = GPA(:,4);
-gps_data.spd_error = GPA(:,6);
-gps_data.hgt_error = GPA(:,5);
+
+maxindex = min(length(GPS),length(GPA));
+
+gps_data.time_us = GPS(1:maxindex,2);
+gps_data.pos_error = GPA(1:maxindex,4);
+gps_data.spd_error = GPA(1:maxindex,6);
+gps_data.hgt_error = GPA(1:maxindex,5);
 
 % set reference point used to set NED origin when GPS accuracy is sufficient
 gps_data.start_index = max(find(gps_data.pos_error < 5.0, 1 ),find(gps_data.spd_error < 1.0, 1 ));
@@ -46,7 +52,7 @@ gps_data.refLLH = [GPS(gps_data.start_index,8);GPS(gps_data.start_index,9);GPS(g
 
 % convert GPS data to NED
 deg2rad = pi/180;
-for index = 1:length(GPS)
+for index = 1:1:maxindex
     if (GPS(index,3) >= 3)
         gps_data.pos_ned(index,:) = LLH2NED([GPS(index,8);GPS(index,9);GPS(index,10)],gps_data.refLLH);
         gps_data.vel_ned(index,:) = [GPS(index,11).*cos(deg2rad*GPS(index,12)),GPS(index,11).*sin(deg2rad*GPS(index,12)),GPS(index,13)];
@@ -56,39 +62,42 @@ for index = 1:length(GPS)
     end
 end
 
+save gps_data.mat gps_data;
+
 %% save range finder data
 clear rng_data;
-rng_data.time_us = RFND(:,2);
-rng_data.dist = RFND(:,3);
+if (exist('RFND','var'))
+    rng_data.time_us = RFND(:,2);
+    rng_data.dist = RFND(:,3);
+    save rng_data.mat rng_data;
+end
 
 %% save optical flow data
 clear flow_data;
-flow_data.time_us = OF(:,2);
-flow_data.qual = OF(:,3)/255; % scale quality from 0 to 1
-flow_data.flowX = OF(:,4); % optical flow rate about the X body axis (rad/sec)
-flow_data.flowY = OF(:,5); % optical flow rate about the Y body axis (rad/sec)
-flow_data.bodyX = OF(:,6); % angular rate about the X body axis (rad/sec)
-flow_data.bodyY = OF(:,7); % angular rate about the Y body axis (rad/sec)
+if (exist('OF','var'))
+    flow_data.time_us = OF(:,2);
+    flow_data.qual = OF(:,3)/255; % scale quality from 0 to 1
+    flow_data.flowX = OF(:,4); % optical flow rate about the X body axis (rad/sec)
+    flow_data.flowY = OF(:,5); % optical flow rate about the Y body axis (rad/sec)
+    flow_data.bodyX = OF(:,6); % angular rate about the X body axis (rad/sec)
+    flow_data.bodyY = OF(:,7); % angular rate about the Y body axis (rad/sec)
+    save flow_data.mat flow_data;
+end
 
 %% save visual odometry data
 clear viso_data;
-viso_data.time_us = VISO(:,2);
-viso_data.dt = VISO(:,3); % time period the measurement was sampled across (sec)
-viso_data.dAngX = VISO(:,4); % delta angle about the X body axis (rad)
-viso_data.dAngY = VISO(:,5); % delta angle about the Y body axis (rad)
-viso_data.dAngZ = VISO(:,6); % delta angle about the Z body axis (rad)
-viso_data.dPosX = VISO(:,7); % delta position along the X body axis (m)
-viso_data.dPosY = VISO(:,8); % delta position along the Y body axis (m)
-viso_data.dPosZ = VISO(:,9); % delta position along the Z body axis (m)
-viso_data.qual = VISO(:,10)/100; % quality from 0 - 1
+if (exist('VISO','var'))
+    viso_data.time_us = VISO(:,2);
+    viso_data.dt = VISO(:,3); % time period the measurement was sampled across (sec)
+    viso_data.dAngX = VISO(:,4); % delta angle about the X body axis (rad)
+    viso_data.dAngY = VISO(:,5); % delta angle about the Y body axis (rad)
+    viso_data.dAngZ = VISO(:,6); % delta angle about the Z body axis (rad)
+    viso_data.dPosX = VISO(:,7); % delta position along the X body axis (m)
+    viso_data.dPosY = VISO(:,8); % delta position along the Y body axis (m)
+    viso_data.dPosZ = VISO(:,9); % delta position along the Z body axis (m)
+    viso_data.qual = VISO(:,10)/100; % quality from 0 - 1
+    save viso_data.mat viso_data;
+end
 
 %% save data and clear workspace
 clearvars -except baro_data imu_data mag_data gps_data rng_data flow_data viso_data;
-
-save baro_data.mat baro_data;
-save imu_data.mat imu_data;
-save mag_data.mat mag_data;
-save gps_data.mat gps_data;
-save rng_data.mat rng_data;
-save flow_data.mat flow_data;
-save viso_data.mat viso_data;