<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;">
<div>
<div>
<div>Kevin,</div>
<div><br>
</div>
<div>You could try the Transform filter. The interface is similar to the transform options in properties, but the results are more stable.</div>
<div><br>
</div>
<div>You can also run the Image Data to Point Set filter to convert to a curvilinear grid and then run the calculator filter with the Coordinate Results option checked and an equation for the transformation set as the expression.</div>
<div><br>
</div>
<div>-Ken</div>
<div><br>
</div>
</div>
</div>
<div><br>
</div>
<span id="OLK_SRC_BODY_SECTION">
<div style="font-family:Calibri; font-size:12pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt">
<span style="font-weight:bold">From: </span>Paraview-developers <<a href="mailto:paraview-developers-bounces@paraview.org">paraview-developers-bounces@paraview.org</a>> on behalf of "Hallock, Kevin" <<a href="mailto:Kevin.Hallock@pfizer.com">Kevin.Hallock@pfizer.com</a>><br>
<span style="font-weight:bold">Date: </span>Monday, April 25, 2016 at 9:41 AM<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:paraview-developers@paraview.org">paraview-developers@paraview.org</a>" <<a href="mailto:paraview-developers@paraview.org">paraview-developers@paraview.org</a>><br>
<span style="font-weight:bold">Subject: </span>[EXTERNAL] [Paraview-developers] Affine transformations in Paraview 5.0.0<br>
</div>
<div><br>
</div>
<span style="mso-bookmark:_MailOriginalBody">
<blockquote id="MAC_OUTLOOK_ATTRIBUTION_BLOCKQUOTE" style="BORDER-LEFT: #b5c4df 5 solid; PADDING:0 0 0 5; MARGIN:0 0 0 5;">
<div>
<meta name="ProgId" content="Excel.Sheet">
<meta name="Generator" content="Microsoft Excel 14">
<link id="Main-File" rel="Main-File" href="file://localhost/Users/hallok02/Library/Caches/TemporaryItems/msoclip/0/clip.htm"><link rel="File-List" href="file://localhost/Users/hallok02/Library/Caches/TemporaryItems/msoclip/0/clip_filelist.xml"><style>
<!--table
{mso-displayed-decimal-separator:"\.";
mso-displayed-thousand-separator:"\,";}
@page
{margin:1.0in .75in 1.0in .75in;
mso-header-margin:.5in;
mso-footer-margin:.5in;}
td
{padding-top:1px;
padding-right:1px;
padding-left:1px;
mso-ignore:padding;
color:black;
font-size:12.0pt;
font-weight:400;
font-style:normal;
text-decoration:none;
font-family:Calibri, sans-serif;
mso-font-charset:0;
mso-number-format:General;
text-align:general;
vertical-align:bottom;
border:none;
mso-background-source:auto;
mso-pattern:auto;
mso-protection:locked visible;
white-space:nowrap;
mso-rotate:0;}
.xl63
{color:black;
font-size:11.0pt;}
-->
</style>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;">
<div>Hi, </div>
<div><br>
</div>
<div>I am trying to display PLY objects that were created from NIFTI files and I know in other software (DSI Studio) the NIFTI images are co-registered by using the header information in the NIFTI file. The matrices that contain the co-registration information
of the two brain atlases are: </div>
<div><br>
</div>
<div>AATG atlas </div>
<div><br>
</div>
<div>
<table border="0" cellpadding="0" cellspacing="0" width="130" style="border-collapse:
collapse;width:130pt">
<!--StartFragment--><colgroup><col width="65" span="2" style="width:65pt"></colgroup>
<tbody>
<tr height="15" style="height:15.0pt">
<td height="15" class="xl63" width="65" style="height:15.0pt;width:65pt">srow_x</td>
<td class="xl63" width="65" style="width:65pt">[-1,0,0,78]</td>
</tr>
<tr height="15" style="height:15.0pt">
<td height="15" class="xl63" style="height:15.0pt">srow_y</td>
<td class="xl63">[0,-1,0,76]</td>
</tr>
<tr height="15" style="height:15.0pt">
<td height="15" class="xl63" style="height:15.0pt">srow_z</td>
<td class="xl63">[0,0,1,-50]</td>
</tr>
<!--EndFragment-->
</tbody>
</table>
<br>
</div>
<div>MNI atlas</div>
<div><br>
</div>
<div>
<table border="0" cellpadding="0" cellspacing="0" width="130" style="border-collapse:
collapse;width:130pt">
<!--StartFragment--><colgroup><col width="65" span="2" style="width:65pt"></colgroup>
<tbody>
<tr height="15" style="height:15.0pt">
<td height="15" class="xl63" width="65" style="height:15.0pt;width:65pt">srow_x</td>
<td class="xl63" width="65" style="width:65pt">[-1,0,0,90]</td>
</tr>
<tr height="15" style="height:15.0pt">
<td height="15" class="xl63" style="height:15.0pt">srow_y</td>
<td class="xl63">[0,1,0,-126]</td>
</tr>
<tr height="15" style="height:15.0pt">
<td height="15" class="xl63" style="height:15.0pt">srow_z</td>
<td class="xl63">[0,0,1,-72]</td>
</tr>
<!--EndFragment-->
</tbody>
</table>
</div>
<div><br>
</div>
<div><br>
</div>
<div>These transforms are supposed to be applied in the following way: </div>
<div><br>
</div>
<div>
<pre style="font-family: 'Courier New', Courier, monospace; font-size: 14.5728px; padding: 1em; border: 1px dashed rgb(140, 172, 187); overflow: auto; widows: 1; background-color: rgb(255, 255, 255);"><p style="margin: 0.5em 0em 1em; line-height: 1.5em;">The (x,y,z) coordinates are given by a general affine transformation<br> of the (i,j,k) indexes:</p><p style="margin: 0.5em 0em 1em; line-height: 1.5em;"> x = srow_x<a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref0" style="color: purple; background-color: transparent;"></a><a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref0" style="color: purple; background-color: transparent;">[0]</a> * i + srow_x<a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref1" style="color: purple; background-color: transparent;"></a><a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref1" style="color: purple; background-color: transparent;">[1]</a> * j + srow_x<a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref2" style="color: purple; background-color: transparent;"></a><a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref2" style="color: purple; background-color: transparent;">[2]</a> * k + srow_x<a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref3" style="color: purple; background-color: transparent;"></a><a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref3" style="color: purple; background-color: transparent;">[3]</a>
y = srow_y<a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref0" style="color: purple; background-color: transparent;"></a><a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref0" style="color: purple; background-color: transparent;">[0]</a> * i + srow_y<a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref1" style="color: purple; background-color: transparent;"></a><a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref1" style="color: purple; background-color: transparent;">[1]</a> * j + srow_y<a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref2" style="color: purple; background-color: transparent;"></a><a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref2" style="color: purple; background-color: transparent;">[2]</a> * k + srow_y<a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref3" style="color: purple; background-color: transparent;"></a><a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref3" style="color: purple; background-color: transparent;">[3]</a>
z = srow_z<a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref0" style="color: purple; background-color: transparent;"></a><a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref0" style="color: purple; background-color: transparent;">[0]</a> * i + srow_z<a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref1" style="color: purple; background-color: transparent;"></a><a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref1" style="color: purple; background-color: transparent;">[1]</a> * j + srow_z<a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref2" style="color: purple; background-color: transparent;"></a><a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref2" style="color: purple; background-color: transparent;">[2]</a> * k + srow_z<a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref3" style="color: purple; background-color: transparent;"></a><a href="http://nifti.nimh.nih.gov/nifti-1/documentation/nifti1fields/nifti1fields_pages/qsform.html#ref3" style="color: purple; background-color: transparent;">[3]</a></p></pre>
</div>
<div><br>
</div>
<div>I thought I would be able to co-register them by applying the above information via the Transform option under Properties, but the result appears to be missing at least one rotation so I am wondering if there is another way to do the affine transformation.
</div>
<div><br>
</div>
<div>Thanks,</div>
<div><br>
</div>
<div>Kevin</div>
</div>
</div>
</blockquote>
</span></span>
</body>
</html>