<div dir="ltr">Hi Steen, I want to ask several questions;<div><br></div><div>1) Do you have a atlas mouse image? I guess you already have one.</div><div>2) Do you have a structure-definition (ROI) file that defines various structures in the atlas I mentioned above (#1). If so, where did it come from? How many structures are defined?</div>
<div>3) If you could successfully transform subject->atlas or atlas->subject, it is straightforward to apply the transformation matrix to the ROI file (#2). If the resolution of the subject and atlas are different, the transformation is most likely two-step: first AIR (linear) and then non-linear (LDDMM). These two matrices can be combined to achieve one-shot transformation. This process is described in the "Getting Started" at <a href="https://www.mristudio.org/wiki/user_manual/diffeomap">https://www.mristudio.org/wiki/user_manual/diffeomap</a>.</div>
<div>4) This transformation should preserve the object list information (as Xin mentioned) but as long as you have a look-up table, you can always decode the meaning of the Object numbers. Please make sure to use "nearest neighbor" interpolation for the ROI file. The assigned number for each structure is arbitrary. You don't create "Object #2" in between "Object #1" and "Object #3" after the ROI file warping.</div>
<div><br></div><div>Please let me know if you have further questions.</div><div><br></div><div>Susumu</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Jan 21, 2014 at 5:55 PM, Pedersen, Steen E. <span dir="ltr"><<a href="mailto:sepeders@texaschildrens.org" target="_blank">sepeders@texaschildrens.org</a>></span> wrote:<br>
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<p class="MsoNormal">Dear Support<u></u><u></u></p>
<p class="MsoNormal"> First, thanks for writing such a powerful and useful set of programs. I have a question regarding the mouse brain atlas maps.
<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">The segmentation of the mouse brain appears very useful. I am processing data from a number of users doing mouse brain. Unfortunately, for each experiment, the exact dimensions of each set of scans can vary as can the mouse age.
<u></u><u></u></p>
<p class="MsoNormal"> I have been using the mouse atlas for registration to a standard mouse so as to compare groups of mice objectively. This is fine, and I can resample the standard mice easily in diffeomap.
<u></u><u></u></p>
<p class="MsoNormal"> My question is whether there is a simple way to resample the segmentation maps for the mouse brain. This would give me a powerful way to quickly get detailed information back to the user. I can resample the raw ROI data,
but I lose the label information (ei – the objects become “object 1, object 2, etc” instead of “hippocampus-L, hippocampus-R, etc”.
<u></u><u></u></p>
<p class="MsoNormal">Other than typing it in each time, is there a way to import the labels into ROIeditor to get them back? I have tried using a new header, but it doesn’t seem to preserve the object labels.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">If there is a more detailed manual for ROIeditor, I would greatly appreciate a pointer for it as I see it being a very useful tool for my work.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thank you,<u></u><u></u></p>
<p class="MsoNormal">Steen Pedersen<u></u><u></u></p>
<p class="MsoNormal">(registered email: <a href="mailto:pedersen@bcm.edu" target="_blank">pedersen@bcm.edu</a>)<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Steen E. Pedersen, Ph.D.<u></u><u></u></p>
<p class="MsoNormal">Associate Professor<u></u><u></u></p>
<p class="MsoNormal">Small Animal Imaging Facility<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Phone: <a href="tel:832-824-3399" value="+18328243399" target="_blank">832-824-3399</a><u></u><u></u></p>
<p class="MsoNormal">Cell: <a href="tel:713-726-0041" value="+17137260041" target="_blank">713-726-0041</a><u></u><u></u></p>
<p class="MsoNormal">email: <a href="mailto:sepeders@texaschildrens.org" target="_blank">sepeders@texaschildrens.org</a><u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Feigin Center, Room C.0200.02<u></u><u></u></p>
<p class="MsoNormal">Texas Childrens Hospital<u></u><u></u></p>
<p class="MsoNormal">1102 Bates St., Houston, TX 77030<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><i><span style="font-size:12.0pt">éala éarendel engla beorhtast<u></u><u></u></span></i></p>
<p class="MsoNormal"><u></u> <u></u></p>
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