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Hi,
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<div class="">The reorient man page explains how to use it with non-linear transformations: <a href="http://cmic.cs.ucl.ac.uk/camino//index.php?n=Man.Reorient" class="">http://cmic.cs.ucl.ac.uk/camino//index.php?n=Man.Reorient</a>.</div>
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<div class="">Danny</div>
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<div class="">On 9 Jan 2015, at 07:32, 穆俊娅 <<a href="mailto:mjy0312@163.com" class="">mjy0312@163.com</a>> wrote:</div>
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<div style="line-height: 150%;" class=""><span lang="EN-US" style="font-size: 12pt; line-height: 150%; font-family: 'Times New Roman', serif;" class=""><b class="">Dear all,</b></span></div>
<div style="line-height: 150%;" class=""><span style="font-family: 'Times New Roman', serif; font-size: 12pt; line-height: 150%;" class=""><b class=""> </b></span><span style="font-family: 'Times New Roman', serif; font-size: 12pt; line-height: 150%;" class=""><b class="">In
the “DWI Registration and Spatial Normalization of DTI†of Camino Tutorials, there is the case study shows how to combine FSL’s flirt program with Camino’s tensor reorientation to perform spatial normalization of diffusion tensor images (using PPD algorithm).</b></span><span style="font-family: 'Times New Roman', serif; font-size: 12pt; line-height: 150%;" class=""><b class=""> </b></span></div>
<div style="line-height: 150%;" class=""><span style="font-family: 'Times New Roman', serif; font-size: 12pt; line-height: 150%;" class=""><b class=""> In that example, the Camino uses the following line to warp the tensor image,</b></span></div>
<p class="MsoNormal" style="line-height:150%"><span lang="EN-US" style="font-size:
12.0pt;line-height:150%;font-family:"Times New Roman","serif"" class=""> </span><span style="font-family: 'Times New Roman', serif; white-space: pre-wrap; line-height: 1.7;" class=""><b class=""><i class="">flirt
-in Control1_DT_Comp${i}.img -applyxfm -init C1C3_Affine.txt -out Control1_DT_Comp${i}_SN.img -ref Control3_FA.img -interp nearestneighbour</i></b></span></p>
<p class="MsoNormal" style="line-height:150%"><span lang="EN-US" style="font-size:
12.0pt;line-height:150%;font-family:"Times New Roman","serif"" class=""> <b class=""> </b></span><span style="font-family: 'Times New Roman', serif; font-size: 12pt; line-height: 150%;" class=""><b class="">and
then uses the following line to reorient the tensors:</b></span></p>
<p class="MsoNormal" style="line-height:150%"><span lang="EN-US" style="font-size:
12.0pt;line-height:150%;font-family:"Times New Roman","serif"" class=""> </span><span style="font-family: 'Times New Roman', serif; white-space: pre-wrap; line-height: 1.7;" class=""><b class=""><i class="">reorient
-trans C1C3_Affine.txt < Control1_DT_SNNR.Bdouble > Control1_DT_SNPPD.Bdouble</i></b></span></p>
<p class="MsoNormal" style="line-height:150%"><span lang="EN-US" style="font-size:
12.0pt;line-height:150%;font-family:"Times New Roman","serif"" class=""><b class=""> </b></span><span style="font-family: 'Times New Roman', serif; font-size: 12pt; line-height: 150%;" class=""><b class="">Here
is my question:</b></span></p>
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<span lang="EN-US" style="font-size:12.0pt;line-height:150%;
font-family:"Times New Roman","serif"" class=""><b class="">Note that reorient will also work with non-linear warps produced by FSL's non-linear registration program fnirt. How we do that?</b></span></div>
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<span style="text-indent: 24pt; font-family: 'Times New Roman', serif; font-size: 12pt; line-height: 150%;" class=""><b class="">In my idea, we need to warp the tensor image by using fnirt. As similar to the above command line in flirt, what is the command
of fnirt? </b></span></div>
<div style="text-indent:24.0pt;mso-char-indent-count:2.0;
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<span style="text-indent: 24pt; font-family: 'Times New Roman', serif; font-size: 12pt; line-height: 150%;" class=""><b class="">After that, to perform reorientation for a non-linear transformation, we then need to use this command?</b></span></div>
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<span lang="EN-US" style="font-family:"Times New Roman","serif";mso-fareast-font-family:
宋体;mso-fareast-theme-font:minor-fareast" class=""> <i class=""><b class=""> reorient -trans Warp.nii -datadims 128 128 60 -voxeldims 1.7 1.7 2.3 < SubjectA_DT_Warp.Bdouble
> SubjectA_DT_WarpPPD.Bdouble</b></i></span></div>
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<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; line-height: normal; text-indent: 15.75pt;" class=""><b class="">I’m looking forward to your response. Feel free to contact me anytime.</b></span></div>
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<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; line-height: normal; text-indent: 15.75pt;" class=""><b class=""> Sincerely,</b></span></div>
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<span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; line-height: normal; text-indent: 15.75pt;" class=""><b class=""> mirabelle</b></span></div>
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