diff --git a/avw2ascii.c b/avw2ascii.c
index f686459bee946fcf4d6c03fcb3aa337b58223732..6c21f3ab40deb5cdacaac9076266f1641e767955 100644
--- a/avw2ascii.c
+++ b/avw2ascii.c
@@ -11,8 +11,8 @@
 /* }}} */
 /* {{{ defines, includes and typedefs */
 
-#include "libss.h"
-#include "libavw.h"
+#include "libss/libss.h"
+#include "libss/libavw.h"
 
 void usage(void);
 
diff --git a/avwcpgeom.c b/avwcpgeom.c
index 61bd7c3f5d5f2517fbd4036d043019266f5aa59f..48056ae873ee750dc5eb0cc7dc29814178d8255d 100644
--- a/avwcpgeom.c
+++ b/avwcpgeom.c
@@ -11,8 +11,8 @@
 /* }}} */
 /* {{{ defines, includes and typedefs */
 
-#include "libss.h"
-#include "libavw.h"
+#include "libss/libss.h"
+#include "libss/libavw.h"
 
 void usage(void);
 
diff --git a/avwcreatehd.c b/avwcreatehd.c
index daa9c019f77575421f69e794e15906869c81c71d..8a9f2ca7315d0b5f876e4b7e2484a2431452a929 100644
--- a/avwcreatehd.c
+++ b/avwcreatehd.c
@@ -11,8 +11,8 @@
 /* }}} */
 /* {{{ defines, includes and typedefs */
 
-#include "libss.h"
-#include "libavw.h"
+#include "libss/libss.h"
+#include "libss/libavw.h"
 
 void usage(void);
 
diff --git a/avwfixfloat.cc b/avwfixfloat.cc
index a0a60692183439029ccae835b9ec528de89ec0c8..94feb6a0e84b0f4bbf45061a91490bb7d935eae8 100644
--- a/avwfixfloat.cc
+++ b/avwfixfloat.cc
@@ -1,7 +1,4 @@
-#include <math.h>
-#include <iostream>
-#include <string>
-#include "newimageall.h"
+#include "newimage/newimageall.h"
 
 using namespace NEWIMAGE;
 
diff --git a/avwhd.c b/avwhd.c
index 6afdbe5923eea25b433a8541da97198bcb598ecb..d22e6171ece671216d064c3970a95628dbe29f87 100644
--- a/avwhd.c
+++ b/avwhd.c
@@ -7,8 +7,8 @@
 /* }}} */
 /* {{{ defines, includes and typedefs */
 
-#include "libss.h"
-#include "libavw.h"
+#include "libss/libss.h"
+#include "libss/libavw.h"
 
 void usage(void);
 
diff --git a/avwmerge.c b/avwmerge.c
index 229b772ad3552bb8ddb5f6af8c46814a783f8b1f..97bb7f66462bfafa405ddf8255df42628e097a96 100644
--- a/avwmerge.c
+++ b/avwmerge.c
@@ -11,11 +11,7 @@
 /* }}} */
 /* {{{ includes */
 
-#include <stdlib.h>
-#include <stdio.h>
-#include <string.h>
 
-#include <avwio.h>
 
 #define MAXINPUTS 10000
 
diff --git a/avwnvols.c b/avwnvols.c
index 2d4efe41202942e743ce27cc758d6329437df8ee..f17bb229ebd63d573d5a454127e799e233f4a6b9 100644
--- a/avwnvols.c
+++ b/avwnvols.c
@@ -7,7 +7,6 @@
 
 /*  CCOPYRIGHT */
 
-#include <avwio.h>
 
 int main(int argc, char **argv)
 {
diff --git a/avwroi.c b/avwroi.c
index 54804d0f3799f9206aaf6949da96f00aa44ba5c9..36efa50d32437a32198867134b29de9634e75fed 100644
--- a/avwroi.c
+++ b/avwroi.c
@@ -11,8 +11,8 @@
 /* }}} */
 /* {{{ defines, includes and typedefs */
 
-#include "libss.h"
-#include "libavw.h"
+#include "libss/libss.h"
+#include "libss/libavw.h"
 
 void usage(void);
 
diff --git a/avwsplit.c b/avwsplit.c
index 5d27f4d7f589d57a11a70348d368ec4ec1edffdc..994473c2d2362131d15cc15a4d7db34221466dc9 100644
--- a/avwsplit.c
+++ b/avwsplit.c
@@ -7,11 +7,7 @@
 
 /*  CCOPYRIGHT */
 
-#include <stdlib.h>
-#include <stdio.h>
-#include <string.h>
 
-#include <avwio.h>
 
 int main(int argc, char **argv)
 {
diff --git a/fslcheck.cc b/fslcheck.cc
index 12eca41782e8ade04fb7b59c52ba677fb0ab4f6f..da1d807dca027e3eb4329cf7eb5c7510d969a1d3 100644
--- a/fslcheck.cc
+++ b/fslcheck.cc
@@ -7,22 +7,13 @@
 /*  CCOPYRIGHT */
 
 
-#include <math.h>
-#include <iostream.h>
-#include <iomanip>
-#include <fstream.h>
-#include <stdlib.h>
-#include <stdio.h>
-#include <string>
-#include <strstream>
-#include <unistd.h>
-
-#include "optimise.h"
-#include "newmatap.h"
-#include "newmatio.h"
-#include "newimageall.h"
-#include "options.h"
-#include "fmribmain.h"
+
+#include "miscmaths/optimise.h"
+#include "newmat/newmatap.h"
+#include "newmat/newmatio.h"
+#include "newimage/newimageall.h"
+#include "utils/options.h"
+#include "newimage/fmribmain.h"
 
 using namespace MISCMATHS;
 using namespace NEWMAT;
diff --git a/fslcomplex.cc b/fslcomplex.cc
index a9d5e90a3fd7020975ef6c0f676615a8e43ffc2d..7a4d5604d7a6f53bf78b06aee1963d77a5db5a0f 100644
--- a/fslcomplex.cc
+++ b/fslcomplex.cc
@@ -6,7 +6,7 @@
 
 /*  CCOPYRIGHT  */
 
-#include "newimageall.h"
+#include "newimage/newimageall.h"
 
 using namespace NEWIMAGE;
 
diff --git a/fslmeants.cc b/fslmeants.cc
index 39fa855aa5f9b5df3bf477fc7026d91b4727e8f5..6317a037f8f0529093e353abc32211391bbed830 100644
--- a/fslmeants.cc
+++ b/fslmeants.cc
@@ -10,8 +10,8 @@
 // Creates a mean time series (ignoring zeros) from the input 4D volume
 // Saves the results as a column in a text file
 
-#include "newimageall.h"
-#include "miscmaths.h"
+#include "newimage/newimageall.h"
+#include "miscmaths/miscmaths.h"
 
 using namespace NEWIMAGE;
 using namespace MISCMATHS;
diff --git a/fslswapdim.cc b/fslswapdim.cc
index bee20db3d6cc3452558ffc5456aaa325ac848a45..e33378762ae12589fe574fb98c8439d37bebf4fc 100644
--- a/fslswapdim.cc
+++ b/fslswapdim.cc
@@ -6,8 +6,8 @@
 
 /*  CCOPYRIGHT  */
 
-#include "newimageall.h"
-#include "fmribmain.h"
+#include "newimage/newimageall.h"
+#include "newimage/fmribmain.h"
 
 using namespace NEWIMAGE;
 
diff --git a/if2avw.c b/if2avw.c
index 7e67dead08302589ce6c1de483d0c6b5cb090384..13ec3e5c2ec2bcd5181c52fc61c545f0b3fc7cd8 100644
--- a/if2avw.c
+++ b/if2avw.c
@@ -11,9 +11,8 @@
 /* }}} */
 /* {{{ defines, includes and typedefs */
 
-#include "libssbase.h"
-#include "avwimage.h"
-#include <assert.h>
+#include "libss/libssbase.h"
+#include "image/avwimage.h"
 
 void usage(void);
 char *find_key(FILE *, char *, const char *);