<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Susumu,<div>The protocol listed here and online have been very useful to me as I attempt to normalize my data. However, even while following these procedures I suffer from the same problems. Namely, when I attempt to register to another subject in my group no changes are made.</div><div><br></div><div>As Siewmin said:</div><div><span class="Apple-style-span" style="font-family: 'Times New Roman'; font-size: 16px; ">"It seems to only work if the template is one of those provided in Landmarker."</span></div><div><br></div><div><div>Any suggestions would be greatly appreciated.</div><div><br></div><div>Additionally, when I use one of the provided templates and save them, I find that they cannot be opened by DTIStudio. The number of slices in the newly created image does not match what is displayed in Landmarker. I understand that it should be resampled to the resolution of the template, but even using these dimensions does not allow for correct display of the images. I have found this to be true for FA images as well as EigenVectors and Tensor images.</div><div><br></div><div>It is possible that I don't have the correct dimensions for importing, but I have tried all that seem logical (given the dimensions of the template and original image). Again, any comments would be very helpful.</div><div><br></div><div>Best,</div><div><br></div><div>Dylan</div><div><br></div><div><br></div><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Dylan Alegria</div><div>CIBSR Imaging RA</div><div>Stanford University</div><div><a href="mailto:dalegria@stanford.edu">dalegria@stanford.edu</a></div><div>(650) 736 0732</div></div></div></div></div></span></div></span> </div><br><div><div>On May 11, 2009, at 11:25 AM, susumu wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div lang="EN-US" link="blue" vlink="blue"><div class="Section1"><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">For those who are interested in image normalization by Landmarker, here I attached a step-by-step instruction.<o:p></o:p></span></font></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Siewmin, I could transform your data with the default setup using this procedure.<o:p></o:p></span></font></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">Susumu<o:p></o:p></span></font></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; "><o:p> </o:p></span></font></div><div><div class="MsoNormal" align="center" style="text-align: center; margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><hr size="2" width="100%" align="center" tabindex="-1"></span></font></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><b><font size="2" face="Tahoma"><span style="font-size: 10pt; font-family: Tahoma; font-weight: bold; ">From:</span></font></b><font size="2" face="Tahoma"><span style="font-size: 10pt; font-family: Tahoma; "><span class="Apple-converted-space"> </span><a href="mailto:mristudio-users-bounces@mristudio.org" style="color: blue; text-decoration: underline; ">mristudio-users-bounces@mristudio.org</a><span class="Apple-converted-space"> </span>[<a href="mailto:mristudio-users-bounces@mristudio.org" style="color: blue; text-decoration: underline; ">mailto:mristudio-users-bounces@mristudio.org</a>]<span class="Apple-converted-space"> </span><b><span style="font-weight: bold; ">On Behalf Of<span class="Apple-converted-space"> </span></span></b>Siewmin Gan<br><b><span style="font-weight: bold; ">Sent:</span></b><span class="Apple-converted-space"> </span>Monday, May 11, 2009 12:21 PM<br><b><span style="font-weight: bold; ">To:</span></b><span class="Apple-converted-space"> </span>DTI Studio, ROI Editor, Landmarker Questions/Support<br><b><span style="font-weight: bold; ">Subject:</span></b><span class="Apple-converted-space"> </span>Re: [Mristudio-users] transformations with AIR in Landmarker</span></font><o:p></o:p></div></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">Hi Susumu, I have learnt a lot from your correspondence, as usual. Will try as you've suggested.<o:p></o:p></span></font></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">Thanks<o:p></o:p></span></font></div></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div></div><div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">Siewmin<o:p></o:p></span></font></div><div><blockquote style="border-top-style: none; border-right-style: none; border-bottom-style: none; border-width: initial; border-color: initial; border-left-style: solid; border-left-color: rgb(204, 204, 204); border-left-width: 1pt; padding-top: 0in; padding-right: 0in; padding-bottom: 0in; padding-left: 6pt; margin-left: 4.8pt; margin-right: 0in; "><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div><div vlink="blue" link="blue"><div><div class="MsoNormal" align="center" style="text-align: center; margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><hr size="2" width="100%" align="center"></span></font></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><b><font size="2" face="Tahoma"><span style="font-size: 10pt; font-family: Tahoma; font-weight: bold; ">From:</span></font></b><font size="2" face="Tahoma"><span style="font-size: 10pt; font-family: Tahoma; "><span class="Apple-converted-space"> </span><a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank" style="color: blue; text-decoration: underline; ">mristudio-users-bounces@mristudio.org</a><span class="Apple-converted-space"> </span>[<a href="mailto:mristudio-users-bounces@mristudio.org" target="_blank" style="color: blue; text-decoration: underline; ">mristudio-users-bounces@mristudio.org</a>] On Behalf Of susumu [<a href="mailto:susumu@mri.jhu.edu" target="_blank" style="color: blue; text-decoration: underline; ">susumu@mri.jhu.edu</a>]<br><b><span style="font-weight: bold; ">Sent:</span></b><span class="Apple-converted-space"> </span>Sunday, May 10, 2009 9:39 AM<br><b><span style="font-weight: bold; ">To:</span></b><span class="Apple-converted-space"> </span>'DTI Studio, ROI Editor, Landmarker Questions/Support'<br><b><span style="font-weight: bold; ">Subject:</span></b><span class="Apple-converted-space"> </span>Re: [Mristudio-users] transformations with AIR in Landmarker</span></font><o:p></o:p></div></div><div><div><div><div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" color="navy" face="Times New Roman"><span style="font-size: 12pt; color: navy; ">Siewmin raised some important points and I hope other users could gain some important information from this thread.</span></font><o:p></o:p></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> I got the mean DWI and tensor file from the original 4D DWI. The tensor file is as you've said, which contains "Dxx, Dyy, Dzz, Dxy, Dxz Dyz" in one file. In Landmarker, I loaded only the mean DWI of the subject and then the tensor file with the "open .d" button. The 4D raw DWI is not used in Landmarker or later. With the "linear" option in AIR, I could rotate the tensor and the mean DWI to the template DWI without having to subsample the input data first. The "nonlinear" option requires the subject data (mean DWI and the tensor file) to be of the same dimension as the template (i.e 181, 217, 181 if ICBM81 DWI is used as template). This is noted in the pop up message, and it would only continue once the input files are resampled to the template. <o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">>It is always advised to do linear transformation first. To start non-linear, you have to make sure that the brain locations and shapes are as similar as possible. This is similar to non-linear fitting. You always have to provide “initial” values close to the real solutions. Otherwise, non-linear fitting could converge to a wrong solution (trapped by “local minima”).</span></font><o:p></o:p></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">Additionally, I tried affine in the linear registration option. The output DWI of the registration is identical to the input of the DWIs if I used one of my subject's DWI as the template. Using the 2nd order polynomial in nonlinear option, an error message occurs "registration terminated due to a calculation problem, please try a lower order model". It seems to only work if the template is one of those provided in Landmarker.<o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> If you can send us two images you are having the problem, we can take a look at why AIR doesn’t work.</span></font><o:p></o:p></p><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">I then saved the rotated tensor file as one file in the .dat format and the linearly registered 3D meanDWI. In MRIview3D, I loaded this new 3D DWI and open this new tensor.dat file with the open.dat button to re-calculates the fa, colour map etc. I viewed the colour map output from this and it looks pretty good, and as described previously.<o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> This is the correct procedure.</span></font><o:p></o:p></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">I saved the fa and principal eigenvector file and used them to perform fiber-tracking. The tracts that are manually extracted obtained looks similiar to the fiber tracts from the original raw 4D DWI.<o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> That is a good sign.</span></font><o:p></o:p></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">The FA values of these tracts are smaller uniformly in comparison, and the assymetry preserved (i.e the left tract FA is smaller than the right tract FA using the maps calculated from the original and rotated tensor).<o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> Normalization requires pixel interpolation, which leads to decreased FA. So you can not compare FA values with and without normalization.</span></font><o:p></o:p></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">If the non-linear option is used, is there a problem that the tensor is subsampled first before it is re-oriented, as described above?<o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> As I mentioned above, nonlinear should be AFTER linear transformation. This means, the data are transformed multiple times and pixels are interpolated multiple times. To avoid this, once you did linear (save transformation matrix: T-linear) and nonlinear (save transformation matrix: T-nonlinear), you can combine the T-linear x T-nonlinear using one of the buttons in the LDDMM section. Once you combined all transformation matrices, you can apply it only once to the original image in the native space.</span></font><o:p></o:p></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> Another interesting thing is, there are two ways to transform images; transform your image to an atlas or transform atlas (usually, binary segmentation map) to your original data for automated segmentation. For the latter approach, you don’t have to transform (therefore interpolate) your original data. When you transform the atlas (segmentation map), make sure to use “nearest neighbor” (no interpolation), not the tri-linear interpolation. The segmentation map consists of arbitrary numbers assigned to each segment (e.g. the internal capsule is “1” and the corona radiata is “3”). If you interpolate these two segments and obtain “2” in between these two segments and if “2” means pons, you would get the pons in between the internal capsule and the corona radiata. On the other hand, when you are transforming your data to an atlas space, use the tri-linear interpolation. Otherwise, you could get strange discontinuity artifacts.</span></font><o:p></o:p></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">Do you suggest using the affine or non-linear transformation of the DWIs and the corresponding transformation of the tensor? Lastly, I'm not sure if the colour map display is of an issue? It occurs both using the linear affine option and the non-linear option.<o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> When everything is working right, the color map should look smooth and clean. Maybe you are using “nearest neighbor” for the tensor transformation?</span></font><o:p></o:p></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">Thanks<o:p></o:p></span></font></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">Siewmin<o:p></o:p></span></font></p><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p><div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">On Sat, May 9, 2009 at 7:44 AM, susumu <<a href="mailto:susumu@mri.jhu.edu" target="_blank" style="color: blue; text-decoration: underline; ">susumu@mri.jhu.edu</a>> wrote:<o:p></o:p></span></font></p><div><div><div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">First, I tried rotating the tensor but had problems with the results. When I look at the colour map from the resulting tensor, it looks ok generally, but there are certain areas of blotchiness and some mixing of colours especially in the sidelines of white matter regions (i.e there can be a striking red line or a blotch of redness in the middle of a green regions within the saggital stratum). These are the steps I took, and would like to check if it is done correctly.<o:p></o:p></span></font></p></div></div><div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">1. resample mean DWI of subject data (together with the 4D DTI data and the tensor) to DWI of ICBM 81 template. Non-linear transform (2nd order trilinear) the resampled meandwi of subject to dwi of template, and used that to drive the transformation of the resampled 4D DTI and the resampled tensor simultaneously. (The resampled tensor was loaded with the .dat button.) I used MRIview 3D to load the normalised 4D DTI, followed by the normalised tensor with the .dat button, and calculate the fa, colour etc maps from the normalised tensor. I tried various thresholding with AIR but the colour maps problem remains.<o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> First of all, I think you don't have to resample DTI images before AIR. AIR can take data with different matrix and pixel sizes and the output images have the same matrix/pixel dimensions as the template (in your case, 181x217x181 of ICBM81).</span></font><o:p></o:p></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> By saying "4D DTI", do you mean raw 4D DWI before tensor calculation? if so, I don't think you want transform raw DWIs. If you want to do anything to raw DTI, you also want to transform the corresponding gradient table, which could be messy. Our tools do not provide methods to transform raw DWIs.</span></font><o:p></o:p></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> When you say, "tensor" data, I assume you are talking about 4D file that contains "Dxx, Dyy, Dzz, Dxy, Dxz, Dyz" images in one file. If so, please make sure that you load this 4D tensor file by the "open .d" button in Landmarker. Once read in Landmarker, the 4D tensor file is disassembled to 6 3D data for Dxx, Dyy, Dzz, Dxy, Dxz, Dyz.</span></font><o:p></o:p></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> Once the AIR is done using mean DWI (your data) - mean DWI (template), the 6 3D tensor element data should be stored all together into one file as a "transformed 4D tensor file".</span></font><o:p></o:p></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> This transformed 4D tensor file needs to be read into DtiStudio to re-calculate new transformed FA, color, vec, etc.</span></font><o:p></o:p></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> The blotch-looking colormap could happen by; 1) transform the color map directly (you should recreate color maps using the recalcuated FA and vector files from the transformed tensor file or 2) you transformed a vector file (transformed vector files should be obtained from the transformed tensor file. Vector can not be directly transformed).</span></font><o:p></o:p></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">Second, I tried without rotating the tensor. I calculate the scalar and colour maps from the original 4D DTI data, aligned the maps to AC-PC line, draw rois on them and invert transform the rois back to native dti space to extract the relevant white matter tracts. I had two problems here. 1) with orienting the subjects scalar DWI to another particular subject's DWI with rigid transformation in AIR and 2) Invert transform ROIs drawn on the registered colour map back to the original DTI space. These are the steps I took:<o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> Maybe you are transforming raw DWI data? Again, you should not transform raw DWI and recalcuate tensor. You have to first calculate tensor (throw away the raw DWIs) and transform the tensor.</span></font><o:p></o:p></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">1. A subject's data which is acquired // to AC-PC is chosen and other subjects not acquired //to AC are registered to this. Again the meanDWI is used for source and target images, this time using rigid transformation in AIR in Landmarker. However, there is no difference detected after the transformation has taken place. However, if I change the target image from a subject's DWI to the mean DWI of the ICBM 81 template, it works but the source data would be subsampled to that of the ICBM template. I'm not sure why it didn't work in the 1st case? <o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> As mentioned above, AIR not only adjust the image orientation and translation, but also the matrix / pixel size..</span></font><o:p></o:p></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> Rigid transformation of AIR is sometimes very cranky. We are working on alternative methods now. please try different threshold or affine.</span></font><o:p></o:p></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">Additionally, using either another subject or the template DWI as target image, would yield the an output file (AlignlinearOutput.air) when the transformation has been performed, which I saved the invert_AlignlinearOutput.air. However, when I clicked on these .air files in the folder it is saved as an installer package, I get the following error message " An error has occurred.The application could not be installed because the AIR file is damaged. Try obtaining a new AIR file from the application author." I have installed the air application and placed it in the same folder, together with the alignlinear.exe file. Is it possible to view the transformation matrix files saved or did I not installed the air application appropriately?<o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> Maybe Xin can answer this question better, but I'm not sure why you want to open *.air??</span></font><o:p></o:p></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> Once you save the *.air, you can load it back to Landmarker and apply to images by using the "open M" button in the LDDMM section.</span></font><o:p></o:p></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">2. ROIs are drawn on the transformed AC-PC aligned colour maps with ROI-editor. I would like to check if it's OK to draw rois on the transformed colour map? These ROIs would later be used as the start ROI and stop ROI to extract the corresponding white matter tract with DTI studio) <o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> Drawing ROIs on color maps is fine. ROI is simply 1/0 information about which pixels you chose and the color maps are simply what is displayed to aid your ROI drawing.</span></font><o:p></o:p></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> If you draw ROI in the atlas space and have a plan to back-transform your ROI files to the native space, there are several things you have to know;</span></font><o:p></o:p></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">1) Atlas space is 1x1x1 and your native space could be 2-3 mm. The ROI defined in the thin 1 mm slice could be lost after transformation to the thick 2-3mm slice. Therefore, you have to create 3D ROIs in the atlas space with at least 3mm thick</span></font><o:p></o:p></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">2) Use nearest neighbor interpolation when you back-transfer. You don't want to get a pixel with 0.3 or 0.4 after transformation. You want 1/0</span></font><o:p></o:p></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; ">3. I tried to invert-transform these ROIs back to the original DTI space with the previously saved invert_matrix.air file. How is that done in Landmarker and if the previous error message needs to be resolved before I can used the matrix files? <o:p></o:p></span></font></p><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="2" color="navy" face="Arial"><span style="font-size: 10pt; font-family: Arial; color: navy; ">> Xin, how to do the invert-transformation of *.air?</span></font><o:p></o:p></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" color="navy" face="Times New Roman"><span style="font-size: 12pt; color: navy; ">Susumu</span></font><o:p></o:p></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div><div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div></div></div><p style="margin-bottom: 12pt; margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><br>_______________________________________________<br>Mristudio-users mailing list<br><a href="mailto:Mristudio-users@mristudio.org" target="_blank" style="color: blue; text-decoration: underline; ">Mristudio-users@mristudio.org</a><br><a href="http://lists.mristudio.org/mailman/listinfo/mristudio-users" target="_blank" style="color: blue; text-decoration: underline; ">http://lists.mristudio.org/mailman/listinfo/mristudio-users</a><o:p></o:p></span></font></p></div><p style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "> <o:p></o:p></span></font></p></div></div></div></div></div></div></div></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div></div></div><div class="MsoNormal" align="center" style="text-align: center; margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><hr size="2" width="100%" align="center"></span></font></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="1" color="gray" face="Arial"><span style="font-size: 7.5pt; font-family: Arial; color: gray; ">This e-mail message (including any attachments) is for the sole use of<br>the intended recipient(s) and may contain confidential and privileged<br>information. If the reader of this message is not the intended<br>recipient, you are hereby notified that any dissemination, distribution<br>or copying of this message (including any attachments) is strictly<br>prohibited.<br><br>If you have received this message in error, please contact<br>the sender by reply e-mail message and destroy all copies of the<br>original message (including attachments).</span></font><o:p></o:p></div></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><br>_______________________________________________<br>Mristudio-users mailing list<br><a href="mailto:Mristudio-users@mristudio.org" style="color: blue; text-decoration: underline; ">Mristudio-users@mristudio.org</a><br><a href="http://lists.mristudio.org/mailman/listinfo/mristudio-users" target="_blank" style="color: blue; text-decoration: underline; ">http://lists.mristudio.org/mailman/listinfo/mristudio-users</a><o:p></o:p></span></font></div></blockquote></div><div style="margin-top: 0in; margin-right: 0in; margin-left: 0in; margin-bottom: 0.0001pt; font-size: 12pt; font-family: 'Times New Roman'; "><font size="3" face="Times New Roman"><span style="font-size: 12pt; "><o:p> </o:p></span></font></div></div><span><siewmin.ppt></span></div>_______________________________________________<br>Mristudio-users mailing list<br><a href="mailto:Mristudio-users@mristudio.org" style="color: blue; text-decoration: underline; ">Mristudio-users@mristudio.org</a><br><a href="http://lists.mristudio.org/mailman/listinfo/mristudio-users" style="color: blue; text-decoration: underline; ">http://lists.mristudio.org/mailman/listinfo/mristudio-users</a><br></div></span></blockquote></div><br></div></body></html>