Please see below;<br><br><div class="gmail_quote"><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>1) I have anatomical images and DTI images, all in DICOM format. And I want to know how to superimpose these two types of images (crop and rescale)?. Here is what I did.I tried to use Diffeomap, I use the "Crop" button to I throw away some axial slices from the anatomical images. Then I use "Resample Image" button, and I enter the dimensions of the DTI image and I get a part of the image (the scaling step was not right? It crops the right and left sides of the image)<br>
</blockquote><div><br>> Crop tool is to prepare two images before submission to non-linear transformation, but not to do resampling. For example, if your image covers only to the level of the midbrain and out atlas is extended to the medulla. Then, non-linear image-matching algorithm (LDDMM) gets confused. In this case, you want to crop the atlas image to the level of the midbrain so that both images covers the same areas of the brains.<br>
> You can match the pixel size and matrix size using the "resample image" tool. However, this works only when; 1) the center of FOV is identical (translation) and 2) the orientation of the FOV is identical (rotation). If T1 and DTI were acquired without changing the center of FOV and it's orientation (and also if the subject motion is negligible), you can co-register two images just by the resample tool<br>
> If your T1 and DTI were not co-registered when they were acquired, you need post-processing registration. There are 1) theoretical registration and 2) registration tool (AIR)<br>> For theoretical registration, you need to extract information about the center of FOV and oblique (rotation) information from DICOM or other types of header information. Then you can type in these information in the "translation" and "rotation" tools in DiffeoMap. <br>
> For registration tool, you need to use "rigid transformation" of AIR. Use DTI (such as b0 or DWI) as a template and register T1 to the template. Here, you can submit T1 image even if the matrix, pixel size, brain positions are different from DTI. The output file has the same dimensions as DTI. This procedure is explained in <a href="https://www.mristudio.org/wiki/user_manual/diffeomap/GetStarted_StepOne_LinearNormalization">https://www.mristudio.org/wiki/user_manual/diffeomap/GetStarted_StepOne_LinearNormalization</a>. As you can see, this could be the easiest way, but please make sure that the output of this automated registration actually worked by carefully inspect the results. If the initial position of the brain in T1 is very different from DTI, it may not work. You many need to use "mutual" registration (it takes much longer) or few-point landmarks (manual but much quicker) for initial alignment or sometimes you need to remove skull intensity. All these operations can be done within DiffeoMap.<br>
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<br>2) When I tried to define some ROIs in the ROIeditor and save my ROI data as "binary maps", then try to open this map in DTI Studio, I get a message that tells me <b>"Unrecognized image-ROI data file!"</b>. I don't know what this means.<br>
</blockquote><div><br>> please use "binary" not "binary map". To learn what is the "binary map" format, please refer to FAQ#16. You need to save an ROI as "binary" in RoiEditor and open is as "binary" in DtiStudio. If you have only 1 ROI, this is the best way. If you have multiple ROIs and you want to combine them with specific operations such as "OR', "AND", "NOT", then you want to use "binary map". You need to save the ROI files as "binary map" in RoiEditor and load as "binary map".<br>
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<br>3) Also, can I define the ROIs and the seeds in the anatomical image then transform it to the DTI images? <br></blockquote><div><br>> Yes, first T1 has to go through DiffeoMap to make sure it is coregistered to DTI and has exactly the same matrix and pixel dimensions (AIR rigid registration could be the easiest way, see above). <br>
> Then load the registered T1 to RoiEditor and define ROIs. If you define one ROI, save and load as "binary". If you draw multiple ROIs and combine them for tractography, use "binary map".<br><br></div>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>By the way, I can not use the brain Atlas that comes with the software, because I'm not dealing with brain data. Thank you.<br>
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<br>Fatma.<br><br>
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