Swizzle dims 3 and 4 for 2dseq without reco files

Bru2.app/Contents/Info.plist

@@ -0,0 +1,45 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+  <key>CFBundleDevelopmentRegion</key>
+  <string>English</string>
+  <key>CFBundleExecutable</key>
+  <string>Bru2</string>
+  <key>CFBundleName</key>
+  <string>Bru2</string>
+  <key>CFBundleIdentifier</key>
+  <string>com.company.Bru2</string>
+  <key>CFBundleInfoDictionaryVersion</key>
+  <string>6.0</string>
+  <key>CFBundlePackageType</key>
+  <string>APPL</string>
+  <key>CFBundleSignature</key>
+  <string>Bru2</string>
+  <key>CFBundleShortVersionString</key>
+  <string>0.1</string>
+  <key>CFBundleVersion</key>
+  <string>1</string>
+  <key>CSResourcesFileMapped</key>
+  <true/>
+  <key>CFBundleDocumentTypes</key>
+  <array>
+    <dict>
+      <key>CFBundleTypeRole</key>
+      <string>Viewer</string>
+      <key>CFBundleTypeExtensions</key>
+      <array>
+        <string>*</string>
+      </array>
+      <key>CFBundleTypeOSTypes</key>
+      <array>
+        <string>fold</string>
+        <string>disk</string>
+        <string>****</string>
+      </array>
+    </dict>
+  </array>
+  <key>NSHighResolutionCapable</key>
+  <true/>
+</dict>
+</plist>

Bru2.app/Contents/MacOS/Bru2

@@ -0,0 +1 @@
+../../../Bru2

Bru2.app/Contents/PkgInfo

@@ -0,0 +1 @@
+APPL????

Bru2Nii.lps

@@ -7,7 +7,7 @@
         <Filename Value="Bru2Nii.lpr"/>
         <IsPartOfProject Value="True"/>
         <CursorPos X="3" Y="16"/>
-        <UsageCount Value="128"/>
+        <UsageCount Value="130"/>
         <Loaded Value="True"/>
         <LoadedDesigner Value="True"/>
       </Unit0>
@@ -20,7 +20,7 @@
         <EditorIndex Value="1"/>
         <TopLine Value="74"/>
         <CursorPos X="15" Y="79"/>
-        <UsageCount Value="128"/>
+        <UsageCount Value="130"/>
         <Loaded Value="True"/>
         <LoadedDesigner Value="True"/>
       </Unit1>
@@ -29,7 +29,7 @@
         <IsPartOfProject Value="True"/>
         <TopLine Value="88"/>
         <CursorPos Y="108"/>
-        <UsageCount Value="127"/>
+        <UsageCount Value="129"/>
       </Unit2>
       <Unit3>
         <Filename Value="convert.pas"/>
@@ -41,9 +41,9 @@
         <Filename Value="common.inc"/>
         <IsVisibleTab Value="True"/>
         <EditorIndex Value="2"/>
-        <TopLine Value="881"/>
-        <CursorPos X="49" Y="907"/>
-        <UsageCount Value="42"/>
+        <TopLine Value="826"/>
+        <CursorPos X="30" Y="831"/>
+        <UsageCount Value="43"/>
         <Loaded Value="True"/>
       </Unit4>
       <Unit5>
@@ -52,130 +52,130 @@
         <EditorIndex Value="3"/>
         <TopLine Value="176"/>
         <CursorPos X="3" Y="32"/>
-        <UsageCount Value="33"/>
+        <UsageCount Value="34"/>
         <Loaded Value="True"/>
       </Unit5>
     </Units>
     <JumpHistory Count="30" HistoryIndex="29">
       <Position1>
         <Filename Value="common.inc"/>
-        <Caret Line="896" Column="19" TopLine="878"/>
+        <Caret Line="799" Column="9" TopLine="784"/>
       </Position1>
       <Position2>
         <Filename Value="common.inc"/>
-        <Caret Line="828" Column="20" TopLine="822"/>
+        <Caret Line="807" Column="7" TopLine="785"/>
       </Position2>
       <Position3>
         <Filename Value="common.inc"/>
-        <Caret Line="829" Column="20" TopLine="822"/>
+        <Caret Line="351" Column="41" TopLine="339"/>
       </Position3>
       <Position4>
         <Filename Value="common.inc"/>
-        <Caret Line="830" Column="20" TopLine="822"/>
+        <Caret Line="376" Column="22" TopLine="354"/>
       </Position4>
       <Position5>
         <Filename Value="common.inc"/>
-        <Caret Line="833" Column="13" TopLine="822"/>
+        <Caret Line="377" Column="29" TopLine="355"/>
       </Position5>
       <Position6>
         <Filename Value="common.inc"/>
-        <Caret Line="242" Column="20" TopLine="237"/>
+        <Caret Line="807" Column="7" TopLine="785"/>
       </Position6>
       <Position7>
         <Filename Value="common.inc"/>
-        <Caret Line="828" Column="20" TopLine="812"/>
+        <Caret Line="340" Column="43" TopLine="339"/>
       </Position7>
       <Position8>
         <Filename Value="common.inc"/>
-        <Caret Line="830" Column="20" TopLine="814"/>
+        <Caret Line="800" TopLine="786"/>
       </Position8>
       <Position9>
         <Filename Value="common.inc"/>
-        <Caret Line="831" Column="20" TopLine="815"/>
+        <Caret Line="810" Column="10" TopLine="790"/>
       </Position9>
       <Position10>
         <Filename Value="common.inc"/>
-        <Caret Line="834" Column="13" TopLine="818"/>
+        <Caret Line="834" Column="5" TopLine="825"/>
       </Position10>
       <Position11>
         <Filename Value="common.inc"/>
-        <Caret Line="278" Column="21" TopLine="270"/>
+        <Caret Line="805" Column="22" TopLine="796"/>
       </Position11>
       <Position12>
         <Filename Value="common.inc"/>
-        <Caret Line="832" Column="74" TopLine="825"/>
+        <Caret Line="794" Column="35" TopLine="792"/>
       </Position12>
       <Position13>
         <Filename Value="common.inc"/>
-        <Caret Line="834" Column="13" TopLine="825"/>
+        <Caret Line="797" Column="19" TopLine="793"/>
       </Position13>
       <Position14>
         <Filename Value="common.inc"/>
-        <Caret Line="284" Column="9" TopLine="265"/>
+        <Caret Line="808" Column="20" TopLine="799"/>
       </Position14>
       <Position15>
         <Filename Value="common.inc"/>
-        <Caret Line="280" Column="48" TopLine="269"/>
+        <Caret Line="838" Column="3" TopLine="832"/>
       </Position15>
       <Position16>
         <Filename Value="common.inc"/>
-        <Caret Line="830" Column="27" TopLine="826"/>
+        <Caret Line="803" Column="12" TopLine="800"/>
       </Position16>
       <Position17>
         <Filename Value="common.inc"/>
-        <Caret Line="869" Column="68" TopLine="862"/>
+        <Caret Line="932" Column="26" TopLine="917"/>
       </Position17>
       <Position18>
         <Filename Value="common.inc"/>
-        <Caret Line="905" Column="16" TopLine="888"/>
+        <Caret Line="283" Column="45" TopLine="275"/>
       </Position18>
       <Position19>
         <Filename Value="common.inc"/>
-        <Caret Line="901" Column="48" TopLine="889"/>
+        <Caret Line="288" Column="51" TopLine="275"/>
       </Position19>
       <Position20>
         <Filename Value="common.inc"/>
-        <Caret Line="883" Column="84" TopLine="858"/>
+        <Caret Line="932" Column="26" TopLine="917"/>
       </Position20>
       <Position21>
         <Filename Value="common.inc"/>
-        <Caret Line="728" Column="66" TopLine="720"/>
+        <Caret Line="279" Column="10" TopLine="275"/>
       </Position21>
       <Position22>
         <Filename Value="common.inc"/>
-        <Caret Line="831" Column="33" TopLine="822"/>
+        <Caret Line="5" Column="93"/>
       </Position22>
       <Position23>
         <Filename Value="common.inc"/>
-        <Caret Line="826" Column="20" TopLine="817"/>
+        <Caret Line="424" Column="60" TopLine="409"/>
       </Position23>
       <Position24>
         <Filename Value="common.inc"/>
-        <Caret Line="873" Column="122" TopLine="860"/>
+        <Caret Line="28" Column="54" TopLine="16"/>
       </Position24>
       <Position25>
         <Filename Value="common.inc"/>
-        <Caret Line="846" Column="19" TopLine="838"/>
+        <Caret Line="936" Column="5" TopLine="919"/>
       </Position25>
       <Position26>
         <Filename Value="common.inc"/>
-        <Caret Line="808" Column="19" TopLine="790"/>
+        <Caret Line="739" Column="20" TopLine="736"/>
       </Position26>
       <Position27>
         <Filename Value="common.inc"/>
-        <Caret Line="858" Column="19" TopLine="837"/>
+        <Caret Line="810" Column="37" TopLine="802"/>
       </Position27>
       <Position28>
         <Filename Value="common.inc"/>
-        <Caret Line="688" Column="15" TopLine="672"/>
+        <Caret Line="26" Column="71" TopLine="20"/>
       </Position28>
       <Position29>
-        <Filename Value="main.pas"/>
-        <Caret Line="79" Column="57" TopLine="62"/>
+        <Filename Value="common.inc"/>
+        <Caret Line="877" Column="7" TopLine="865"/>
       </Position29>
       <Position30>
         <Filename Value="common.inc"/>
-        <Caret Line="896" Column="37" TopLine="878"/>
+        <Caret Line="795" Column="20" TopLine="782"/>
       </Position30>
     </JumpHistory>
   </ProjectSession>

common.inc

@@ -23,7 +23,7 @@ type
   end;
   TMat = array[1..4, 1..4] of single;
   TBrukerHdr = Record
-    RECO_byte_order_little, RECO_transposition_varies: boolean;
+    RECO_byte_order_little, RECO_transposition_varies, has_d3proc_file: boolean;
     RECO_transposition, RECO_wordtype_bits, ACQ_ns_list_size, ACQ_nr_completed, ACQ_NR, ACQ_NI, ACQ_NSLICES, METHOD_PVM_ObjOrderScheme: integer;
     RECO_map_offset, RECO_map_slope,   ACQ_RG, ACQ_slice_thick,ACQ_read_offset, ACQ_phase1_offset, METHOD_slice_offset, METHOD_slice_distance: single;
     METHOD_PVM_SpatResol,RECO_offset, RECO_size, RECO_fov, ACQ_grad_matrix, ACQ_slice_sepn, ACQ_repetition_time : TVec;
@@ -787,13 +787,39 @@ begin
          wp^[i] := swap(wp^[i]);
 end;
 
-procedure CpyImg (lRawFName, lNiiFName: string; ImgBytes: integer; BrHdr: TBrukerHdr);
+procedure SwapDimsZT(p: Pointer; ImgBytes: integer; lNiHdr: TNiHdr);
+//swizzle 3rd and 4th dimensions
+type
+    ByteRA0 = array [0..0] of byte;
+    Bytep0 = ^ByteRA0;
+var
+    xyBytes, xyzBytes, z, t, posIn, posOut: integer;
+    pIn, pOut: Bytep0;
+begin
+     xyBytes := lNiHdr.dim[1]*lNiHdr.dim[2]*(lNiHdr.bitpix div 8);
+     if (lNiHdr.dim[3] < 2) or (lNiHdr.dim[4] < 2) or ((xyBytes*lNiHdr.dim[3]*lNiHdr.dim[4]) <> ImgBytes) then exit;
+     xyzBytes := xyBytes * lNiHdr.dim[3];
+     getmem(pIn, ImgBytes);
+     Move(p^,pIn^,ImgBytes);//src, dest, bytes
+     pOut := Bytep0(p);
+     posIn := 0;
+     for z := 1 to lNiHdr.dim[3] do begin
+       for t := 1 to lNiHdr.dim[4] do begin
+           posOut := ((t-1)*xyzBytes) + ((z-1) * xyBytes);
+           Move(pIn^[posIn],pOut^[posOut], xyBytes);//src, dest, bytes
+           inc(posIn, xyBytes);
+       end;
+     end;
+     freemem(pIn);
+end;
+
+procedure CpyImg (lRawFName, lNiiFName: string; ImgBytes: integer; BrHdr: TBrukerHdr; lNiHdr: TNiHdr);
 //copy image data from Bruker 2dseq file to NIfTI .nii file: forces native byte order
 var
   lOutF,lInF: File of byte;
   p: Pointer;
 begin
-   getmem(p, ImgBytes);
+  getmem(p, ImgBytes);
   AssignFile(lInF, lRawFName);
   Reset(lInF);
   FileMode := 0; //Set file access to read only
@@ -810,6 +836,8 @@ begin
     if (BrHdr.RECO_wordtype_bits = 16) then
        Swap16(p, ImgBytes);
   end;  //swap image data to have native endian
+  if BrHdr.has_d3proc_file then //based on one image from Mikaël Naveau
+    SwapDimsZT(p, ImgBytes, lNiHdr);
   AssignFile(lOutF, lNiiFName);
   Reset(lOutF);
   Seek(lOutF, sizeof(TNiHdr));
@@ -843,11 +871,11 @@ begin
   if not BrReadACQP(lAcqpFName, BrHdr) then exit;
   if not BrReadRECO(lRecoFName, BrHdr) then exit;
   BrReadMETHOD(lMethodFName, BrHdr);
-  if fileexists(ExtractFilePath(lImgFName)+ 'd3proc') then begin
+  BrHdr.has_d3proc_file := fileexists(ExtractFilePath(lImgFName)+ 'd3proc');
+  if BrHdr.has_d3proc_file then begin
      showmsg('Found "d3proc" file: assuming 32-bit data');
      BrHdr.RECO_wordtype_bits := 32;
   end;
-
   //Label files based on EXPNO and PROCNO: ACQP is in EXPNO directory 2dSeq in PROCNO directory
   if lOutFName = '' then
      lOutFName := ExtractFilePath(lAcqpFName)+'X'+Extractfilename(ExtractFileDir(lAcqpFName))+'P'+ Extractfilename(ExtractFileDir(lImgFName))+'.nii'
@@ -866,7 +894,7 @@ begin
   BrReport(BrHdr, lRecoFName, lOutFName, lVerbose);
   BrMat (BrHdr, NiHdr, lFOVx10, lVerbose);
   SaveNiHdr (lOutFName, NiHdr);
-  CpyImg (lImgFName, lOutFName, ImgBytes, BrHdr);
+  CpyImg (lImgFName, lOutFName, ImgBytes, BrHdr, NiHdr);
 end;
 
 procedure Find2Dseq(Dir, OutFName: string; FOVx10, lVerbose, OnlyConvert3D, AppendProtocolName: boolean; var nOK: integer);