Hi Salvador,<div><br></div><div>AIR/MI registration is a common procedure for human MRI because of two reasons. First, they tend to move (more than 1 pixel). Second, human scanners have larger eddy current, which shifts and deforms the images. To remove these registration errors, we use the co-registration tools. I believe it is not necessary for animal studies because they are sedated and heads are fixed.</div>
<div><br></div><div>After the co-registration process, we inevitably apply pixel interpolation, which reduces resolution and enhances SNR. So, that could be one of the reasons why the images look different. I guess if you skip the registration, the images look much similar.</div>
<div><br></div><div>Just one note; we have DiffeoMap and RoiEditor you can download from <a href="http://www.mristudio.org">www.mristudio.org</a>, which allows you to do cross-contrast and cross-animal registration.</div>
<div><br></div><div>Susumu<br><br><div class="gmail_quote">On Thu, Feb 3, 2011 at 10:09 AM, Castaneda, Salvador <span dir="ltr"><<a href="mailto:salvador.castaneda@med.uni-tuebingen.de">salvador.castaneda@med.uni-tuebingen.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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<div dir="ltr" align="left"><span><font face="Arial" color="#0000ff" size="2">Hello Mri studio users,</font></span></div>
<div dir="ltr" align="left"><span><font face="Arial" color="#0000ff" size="2"></font></span> </div>
<div dir="ltr" align="left"><span><font face="Arial" color="#0000ff" size="2">I am working with a MRI scanner with bruker hardware and
siemens software. I acquire mosaic files and have been able to work with the
mosaic in DTI studio to then do a AIR registration. I produce whatever maps i
need. It works great. I then, upload the maps created by DTI studio to another
imaging software called PMOD, as Analize files, for coregistration with
a T2W rat brain Anatomy image. I am able produce good quality ROIs of the
brain areas i need. Just recently i have discovered, that the MR can also
provide for me the FA, TRACE, DWI, and ADC maps as DICOMs. These I can also
upload to Pmod for coregistration with the anatomy. So theoretically I can
choose to do this, but i have noticed that the quality of the maps produced by
the MR software are somehow "lacking". So my question is : Is the AIR and mutual
image registration in DTI studio crutial for the processing of the data from the
MR? I like the images produced by DTI studio better, but what is the basis of
the improvement? how is it different to the images calculated by the MR?
The MR software is Siemens Syngo. I know that DTI studio also provides
tractography which makes a better tool for this analisis, but if i would be just
interested inthe FA maps, are the images produced by the scanner enough?
(regarding affine coregistration)</font></span></div>
<div dir="ltr" align="left"><span><font face="Arial" color="#0000ff" size="2">thanks in advance for your responses. </font></span></div>
<div dir="ltr" align="left"><span><font face="Arial" color="#0000ff" size="2"></font></span> </div><font color="#888888">
<div dir="ltr" align="left"><span><font face="Arial" color="#0000ff" size="2">Salvador</font></span></div></font></div>
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