<div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><div style="line-height: 150%;"><span lang="EN-US" style="font-size: 12pt; line-height: 150%; font-family: 'Times New Roman', serif;"><b>Dear all,</b></span></div><div style="line-height: 150%;"><span style="font-family: 'Times New Roman', serif; font-size: 12pt; line-height: 150%;"><b> </b></span><span style="font-family: 'Times New Roman', serif; font-size: 12pt; line-height: 150%;"><b>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%;"><b> </b></span></div><div style="line-height: 150%;"><span style="font-family: 'Times New Roman', serif; font-size: 12pt; line-height: 150%;"><b> 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""> </span><span style="font-family: 'Times New Roman', serif; white-space: pre-wrap; line-height: 1.7;"><b><i>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""> <b> </b></span><span style="font-family: 'Times New Roman', serif; font-size: 12pt; line-height: 150%;"><b>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""> </span><span style="font-family: 'Times New Roman', serif; white-space: pre-wrap; line-height: 1.7;"><b><i>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""><b> </b></span><span style="font-family: 'Times New Roman', serif; font-size: 12pt; line-height: 150%;"><b>Here is my
question:</b></span></p>
<div style="text-indent:24.0pt;mso-char-indent-count:2.0;
line-height:150%"><span lang="EN-US" style="font-size:12.0pt;line-height:150%;
font-family:"Times New Roman","serif""><b>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><div style="text-indent:24.0pt;mso-char-indent-count:2.0;
line-height:150%"><span style="text-indent: 24pt; font-family: 'Times New Roman', serif; font-size: 12pt; line-height: 150%;"><b>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;
line-height:150%"><span style="text-indent: 24pt; font-family: 'Times New Roman', serif; font-size: 12pt; line-height: 150%;"><b>After that, to perform reorientation for a non-linear transformation,
we then need to use this command?</b></span></div><div style="text-indent:24.0pt;mso-char-indent-count:2.0;
line-height:150%"><span style="text-indent: 24pt; font-family: 'Times New Roman', serif; font-size: 12pt; line-height: 150%;"><br></span></div>
<div style="margin: 0cm 0cm 0.0001pt; line-height: 14.65pt; background-position: initial initial; background-repeat: initial initial;"><span lang="EN-US" style="font-family:"Times New Roman","serif";mso-fareast-font-family:
ËÎÌå;mso-fareast-theme-font:minor-fareast"> <i><b> 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><div style="margin: 0cm 0cm 0.0001pt; line-height: 14.65pt; background-position: initial initial; background-repeat: initial initial;"><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; line-height: normal; text-indent: 15.75pt;"><b>I¡¯m looking forward to your response. Feel free to contact me anytime.</b></span></div><div style="margin: 0cm 0cm 0.0001pt; line-height: 14.65pt; background-position: initial initial; background-repeat: initial initial;"><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; line-height: normal; text-indent: 15.75pt;"><b> Sincerely,</b></span></div><div style="margin: 0cm 0cm 0.0001pt; line-height: 14.65pt; background-position: initial initial; background-repeat: initial initial;"><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; line-height: normal; text-indent: 15.75pt;"><b> mirabelle</b></span></div></div><br><br><span title="neteasefooter"><span id="netease_mail_footer"></span></span>