<div dir="ltr">Hi Nida,<div><br></div><div style>I hope #7 and #11 in the "Getting Started" of this page (<a href="https://www.mristudio.org/wiki/user_manual/diffeomap">https://www.mristudio.org/wiki/user_manual/diffeomap</a>) answer some of your questions.</div>
<div style><br></div><div style>Because you did 3-alpha transformation, you get Ki001/Ki002/Ki003 and Kimap. Ki001-003 are recorded for each alpha step. For example, if you did alpha = 0.01/0.005/0.002, Ki001 gives you a transformation with alpha=0.01. If you combine Ki001+Ki002, then you can create an image after alpha = 0.01+0.005. Ki001+002+003 = Kimap. So, if you want a result after all three iterations of different alpha values (elasticity), you simply use Kimap.</div>
<div style><br></div><div style>If you use Kimap, your patient images become similar to our atlas. If you superimpose our WMPM (changed the name to BPM recently) and if the transformation is successful, you should see accurate parcellation.</div>
<div style><br></div><div style>Conversely, you can transform BPM by using Hmap (as explained in the #11 above), you need to use nearest neighbor for this transformation. In this way, the parcellation map is transformed to the shape of the patient in the native space.</div>
<div style><br></div><div style>If you see poor matching between the image and the parcellation map, common mistakes are;</div><div style><br></div><div style>> transformation was not accurate because the initial linear registration results are poor. You may need to do skull stripping or landmark-driven initial alignment. Our Mutual Information option, instead of AIR, often performs better.</div>
<div style>> you used Hmap, not Kimap to the patient image and applied the atlas-space BPM or you used Kimap, not Hmap, to the BPM and applied to the native space patient image.</div><div style><br></div><div style>If you send me an image showing how bad the parcellation by BPM, I may be able to tell why.</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sun, May 12, 2013 at 10:47 AM, Nida Sajjad <span dir="ltr"><<a href="mailto:nidasajjad958@hotmail.com" target="_blank">nidasajjad958@hotmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div dir="ltr"><br><br><div><div></div><hr><br><br>
<div dir="ltr">Dear All,<div><div class="h5"><br>I am sorry may be i am not able to explain my problem exactly. The data you are seeing in attached files is just from some tutorial its not my original data. i was just trying to explain that i am following thee steps as mentioned in the pictures. After multichanel processing of my data, i got results which contain following files: <br>
finalMetricDistance,<br>Hmap.vtk, <br>Hmap_001.vtk<br>Hmap_002.vtk<br>Hmap_003.vtk<br>,identity,<br>Kimap.vtk <br>Kimap_001.vtk<br>Kimap_002.vtk <br>Kimap_003.vtk <br>lddmm-vmm1.conf <br>lddmm-vmm2.conf <br>lddmm-vmm3.conf <br>
LocalAddress <br> stdout <br>Target1.img <br>Target2.img <br>Template1.img<br>Template2.img<br>Now when i want to use my Updated FA in Roi editor and upload Rois they are not fully fit to my data. How can i use the above mentioned processed data in Roi editor. This is what i want to ask. And also that the roi statistics contain pixel value , min max and mean and std deviation. Are these the FA values for each Roi?<br>
<br>I hope now i am able to make my self clear.<br>Thank you much<br><br>Regards,<br>Nida<br><br><br><br><br><br><br><br><div><div></div><hr><br></div> </div></div></div></div> </div></div>
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