<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div style="RIGHT: auto">Hi all,</div>
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<DIV style="RIGHT: auto" id=yiv884731202yui_3_2_0_14_132455675939085>Just looking for a bit of help in using diffeomap as I seem to be doing something wrong in converting the Talairach_SS_WMPM to the native subject space. When I apply the Hmap from the LDDMM analysis to the WMPM the WMPM is converted perfectly. When I then apply the inverted AIR file I am running into a problem. The file does not seem to convert it correctly. </DIV>
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<DIV id=yiv884731202yui_3_2_0_14_13245567593901915>I have searched through the forum and applied the approach suggested in a couple of posts but I am still having the same issue. If anyone has experience of this and could help me out it would be much appreciated.</DIV>
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<DIV id=yiv884731202yui_3_2_0_14_13245567593903557>The atlas is 192*192*136 while my data is 256*256*55. When I apply the Inverted air file the WMPM gets converted but seems to remain in the original dimensions. For example, there are originally 136 slices and the air_inverted file also has 136 slices but <VAR id=yiv884731202yui-ie-cursor></VAR>an image occurs in only 55 of them. The image is also compressed to the bottom right of the frame.</DIV>
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<div style="MARGIN: 0cm 0cm 10pt" class=MsoNormal><SPAN lang=EN-IE><FONT face=Calibri>Procedure<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></FONT></SPAN></div>
<div style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 36pt; RIGHT: auto; mso-list: l0 level1 lfo1" class=MsoListParagraphCxSpFirst><SPAN><SPAN style="RIGHT: auto; mso-list: Ignore">·<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT face=Calibri>Load Template<o:p></o:p></FONT></SPAN></div>
<div style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 72pt; mso-add-space: auto; mso-list: l0 level2 lfo1" class=MsoListParagraphCxSpMiddle><SPAN><SPAN style="mso-list: Ignore">o<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT face=Calibri>Talairach b0<o:p></o:p></FONT></SPAN></div>
<div style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 36pt; mso-list: l0 level1 lfo1" class=MsoListParagraphCxSpMiddle><SPAN><SPAN style="mso-list: Ignore">·<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT face=Calibri>Load Sample<o:p></o:p></FONT></SPAN></div>
<div style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 72pt; mso-add-space: auto; mso-list: l0 level2 lfo1" class=MsoListParagraphCxSpMiddle><SPAN><SPAN style="mso-list: Ignore">o<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT face=Calibri>b0<o:p></o:p></FONT></SPAN></div>
<div style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 72pt; mso-add-space: auto; mso-list: l0 level2 lfo1" class=MsoListParagraphCxSpMiddle><SPAN><SPAN style="mso-list: Ignore">o<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT face=Calibri>FA<o:p></o:p></FONT></SPAN></div>
<div style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 36pt; mso-list: l0 level1 lfo1" class=MsoListParagraphCxSpMiddle><SPAN><SPAN style="mso-list: Ignore">·<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT face=Calibri>Run AIR LINEAR<o:p></o:p></FONT></SPAN></div>
<div style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 72pt; mso-add-space: auto; mso-list: l0 level2 lfo1" class=MsoListParagraphCxSpMiddle><SPAN><SPAN style="mso-list: Ignore">o<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT face=Calibri>Ensure both b0 images active<o:p></o:p></FONT></SPAN></div>
<div style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 72pt; mso-add-space: auto; mso-list: l0 level2 lfo1" class=MsoListParagraphCxSpMiddle><SPAN><SPAN style="mso-list: Ignore">o<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT face=Calibri>Affine/Trilinear<o:p></o:p></FONT></SPAN></div>
<div style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 72pt; mso-add-space: auto; mso-list: l0 level2 lfo1" class=MsoListParagraphCxSpMiddle><SPAN><SPAN style="mso-list: Ignore">o<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT face=Calibri>Save .air file<o:p></o:p></FONT></SPAN></div>
<div style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 72pt; RIGHT: auto; mso-add-space: auto; mso-list: l0 level2 lfo1" class=MsoListParagraphCxSpMiddle><SPAN><SPAN style="mso-list: Ignore">o<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT face=Calibri>Save converted files<o:p></o:p></FONT></SPAN></div>
<div style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 36pt; mso-list: l0 level1 lfo1" class=MsoListParagraphCxSpMiddle><SPAN><SPAN style="mso-list: Ignore">·<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT face=Calibri>Run air invert_air_file<o:p></o:p></FONT></SPAN></div>
<div style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 72pt; RIGHT: auto; mso-add-space: auto; mso-list: l0 level2 lfo1" class=MsoListParagraphCxSpMiddle><SPAN><SPAN style="mso-list: Ignore">o<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT style="RIGHT: auto" face=Calibri>Choose saved air file<o:p></o:p></FONT></SPAN></div>
<div style="TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 36pt; RIGHT: auto; mso-list: l0 level1 lfo1" class=MsoListParagraphCxSpMiddle><SPAN><SPAN style="mso-list: Ignore">·<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT face=Calibri>Close Diffeomap<o:p></o:p></FONT></SPAN></div>
<div style="MARGIN: 0cm 0cm 0pt 36pt" class=MsoListParagraphCxSpMiddle><SPAN lang=EN-IE><o:p><FONT face=Calibri> </FONT></o:p></SPAN></div>
<div style="LINE-HEIGHT: normal; TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 36pt; mso-add-space: auto; mso-list: l0 level1 lfo1" class=MsoListParagraphCxSpMiddle><SPAN><SPAN style="mso-list: Ignore">·<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT face=Calibri>Open Template in Diffeomap<o:p></o:p></FONT></SPAN></div>
<div style="LINE-HEIGHT: normal; TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 72pt; RIGHT: auto; mso-add-space: auto; mso-list: l0 level2 lfo1" class=MsoListParagraphCxSpMiddle><SPAN style="RIGHT: auto"><SPAN style="mso-list: Ignore">o<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN></SPAN><SPAN style="RIGHT: auto"><FONT style="RIGHT: auto" face=Calibri>Open FA image as subject (2<SUP>nd</SUP> time use <VAR id=yui-ie-cursor></VAR>WMPM of Talairach)<o:p></o:p></FONT></SPAN></div>
<div style="LINE-HEIGHT: normal; TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 72pt; mso-add-space: auto; mso-list: l0 level2 lfo1" class=MsoListParagraphCxSpMiddle><SPAN><SPAN style="mso-list: Ignore">o<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT face=Calibri>Select Load Transformation Matrix<o:p></o:p></FONT></SPAN></div>
<div style="LINE-HEIGHT: normal; TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 72pt; mso-add-space: auto; mso-list: l0 level2 lfo1" class=MsoListParagraphCxSpMiddle><SPAN><SPAN style="mso-list: Ignore">o<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT face=Calibri>Choose inverted file air<o:p></o:p></FONT></SPAN></div>
<div style="LINE-HEIGHT: normal; TEXT-INDENT: -18pt; MARGIN: 0cm 0cm 0pt 72pt; RIGHT: auto; mso-add-space: auto; mso-list: l0 level2 lfo1" class=MsoListParagraphCxSpLast><SPAN><SPAN style="mso-list: Ignore">o<SPAN style="FONT: 7pt 'Times New Roman'"> </SPAN></SPAN><FONT face=Calibri>Choose Trilinear or Nearest Neighbour<o:p></o:p></FONT></SPAN></div></DIV>
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<DIV style="RIGHT: auto"> If required I can send the results I have gotten from the process. </DIV>
<DIV id=yiv884731202yui_3_2_0_14_13245567593902592>Thank you in advance,</DIV>
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<DIV id=yiv884731202yui_3_2_0_14_13245567593902695>Bill</DIV></DIV></DIV></DIV></DIV></DIV></DIV><BR><BR></DIV></DIV></div></body></html>