<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"><SPAN style="RIGHT: auto">Hi Xin,</SPAN></div>
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<div style="RIGHT: auto"><SPAN style="RIGHT: auto">Thank you very much, the problem was my selection of the template as you described.<VAR id=yui-ie-cursor></VAR></SPAN></div>
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<div style="RIGHT: auto"><SPAN style="RIGHT: auto">Thanks again for a quick and effective response.</SPAN></div>
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<div style="RIGHT: auto"><SPAN style="RIGHT: auto">Bill</SPAN></div>
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<DIV style="BORDER-BOTTOM: #ccc 1px solid; BORDER-LEFT: #ccc 1px solid; PADDING-BOTTOM: 0px; LINE-HEIGHT: 0; MARGIN: 5px 0px; PADDING-LEFT: 0px; PADDING-RIGHT: 0px; HEIGHT: 0px; FONT-SIZE: 0px; BORDER-TOP: #ccc 1px solid; BORDER-RIGHT: #ccc 1px solid; PADDING-TOP: 0px" class=hr contentEditable=false readonly="true"></DIV><B><SPAN style="FONT-WEIGHT: bold">From:</SPAN></B> Xin Li <xli16@jhmi.edu><BR><B><SPAN style="FONT-WEIGHT: bold">To:</SPAN></B> Bill Quinn <billquinndme@yahoo.com>; "DTI Studio, ROI Editor, DiffeoMap Questions/Support" <mristudio-users@mristudio.org> <BR><B><SPAN style="FONT-WEIGHT: bold">Sent:</SPAN></B> Friday, 23 December 2011, 14:17<BR><B><SPAN style="FONT-WEIGHT: bold">Subject:</SPAN></B> Re: [Mristudio-users] DiffeoMap - Returning Image to the native subject space after LDDMM<BR></FONT><BR>Hello Bill,<BR><BR>Your original data is 256*256*55. When the template is your original data (256*256*55) and the inverted
air is applied, the WMPM is supposed to be converted to your original data space that is 256*256*55. <BR><BR>Please take a look at the second slide on the webpage <A href="https://www.mristudio.org/wiki/user_manual/diffeomap/GetStarted_DualChannelNormalizationPipeline%3A" target=_blank>https://www.mristudio.org/wiki/user_manual/diffeomap/GetStarted_DualChannelNormalizationPipeline%3A</A><BR>It shows the steps to convert the WMPM to the original data space.<BR><BR><BR>By the way, when the WMPM is applied, please make sure to choose nearest neighbor as the interpolation method.<BR><BR><BR>Xin<BR><BR><BR>----- Original Message -----<BR>From: Bill Quinn <<A href="mailto:billquinndme@yahoo.com" ymailto="mailto:billquinndme@yahoo.com">billquinndme@yahoo.com</A>><BR>Date: Friday, December 23, 2011 7:48 am<BR>Subject: Re: [Mristudio-users] DiffeoMap - Returning Image to the native subject space after LDDMM<BR>To: "<A
href="mailto:mristudio-users@mristudio.org" ymailto="mailto:mristudio-users@mristudio.org">mristudio-users@mristudio.org</A>" <<A href="mailto:mristudio-users@mristudio.org" ymailto="mailto:mristudio-users@mristudio.org">mristudio-users@mristudio.org</A>><BR><BR><BR>> Hi all,<BR>> <BR>> <BR>> Just looking for a bit of help in using diffeomap as I seem to be <BR>> doing something wrong in converting the Talairach_SS_WMPM to the <BR>> native subject space. When I apply the Hmap from the LDDMM analysis to <BR>> the WMPM the WMPM is converted perfectly. When I then apply the <BR>> inverted AIR file I am running into a problem. The file does not seem <BR>> to convert it correctly. <BR>> <BR>> I have searched through the forum and applied the approach suggested <BR>> in a couple of posts but I am still having the same issue. If anyone <BR>> has experience of this and could help me out
it would be much appreciated.<BR>> <BR>> The atlas is 192*192*136 while my data is 256*256*55. When I apply <BR>> the Inverted air file the WMPM gets converted but seems to remain in <BR>> the original dimensions. For example, there are originally 136 slices <BR>> and the air_inverted file also has 136 slices but an image occurs in <BR>> only 55 of them. The image is also compressed to the bottom right of <BR>> the frame.<BR>> <BR>> Procedure<BR>> · Load Template<BR>> o Talairach b0<BR>> · Load Sample<BR>> o b0<BR>> o FA<BR>> · Run AIR LINEAR<BR>> o Ensure both b0 images active<BR>> o Affine/Trilinear<BR>>
o Save .air file<BR>> o Save converted files<BR>> · Run air invert_air_file<BR>> o Choose saved air file<BR>> · Close Diffeomap<BR>> <BR>> · Open Template in Diffeomap<BR>> o Open FA image as subject (2nd time use WMPM of Talairach)<BR>> o Select Load Transformation Matrix<BR>> o Choose inverted file air<BR>> o Choose Trilinear or Nearest Neighbour<BR>> <BR>> If required I can send the results I have gotten from the process. <BR>> Thank you in advance,<BR>> Bill<BR>> _______________________________________________<BR>> mristudio-users mailing list<BR>> <A
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