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Subject: Re: [ITK-users] [ITK] using MHA file to store additional information about image
From: Andras Lasso <lasso () queensu ! ca>
Date: 2018-05-31 2:59:25
Message-ID: YQBPR0101MB1859014DCF1236011150DD7BD8630 () YQBPR0101MB1859 ! CANPRD01 ! PROD ! OUTLOOK ! COM
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Yes, Plus toolkit has been using mha and nrrd files for many years to store tracked \
ultrasound data in a single file. Recently we use nrrd format more, as this format \
supports 3D+t image sequences more cleanly. At the beginning, we used ITK's \
reader/writer, but metadata handling was not fast enough and we also needed dynamic \
header construction and memory-cached compressed streaming image I/O. We are now also \
adding support for lossy video codecs as non-standard extensions.
Plus can reconstruct volumes from tracked ultrasound slices, connect to many \
ultrasound devices through native interfaces, connect to most optical and \
electromagnetic trackers, stream tracked ultrasound data through OpenIGTLink for \
real-time visualization to various applications, perform spatial and temporal \
calibrations, etc. Check out www.plustoolkit.org<http://www.plustoolkit.org> and \
www.slicerigt.org<http://www.slicerigt.org> for details. There is a resident Plus \
expert at Robarts, Adam Rankin, you can contact him if you need more information, and \
we'll have a one-week hackathon at Robarts in July where you can meet several \
experienced Plus and SlicerIGT users and developers \
(https://na-mic.github.io/ProjectWeek/PW29_2018_London_Canada/).
Andras
From: Community <community-bounces@itk.org> On Behalf Of Dženan Zukic
Sent: Wednesday, May 30, 2018 4:26 PM
To: Andrew Harris <aharr8@uwo.ca>
Cc: Insight-users <insight-users@itk.org>
Subject: Re: [ITK] [ITK-users] using MHA file to store additional information about \
image
Hi Andrew,
you can add content to image's MetaData dictionary. But you should look at how Plus \
does it (code<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub. \
com%2FPlusToolkit%2FPlusLib%2Fblob%2Fmaster%2Fsrc%2FPlusCommon%2FIO%2FvtkPlusMetaImage \
SequenceIO.cxx&data=02%7C01%7Classo%40queensu.ca%7C5a34db5cc49149f2b77b08d5c66b8a59%7C \
d61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636633087559034726&sdata=9JCBbDgxqHogvLhKlhy8Vnk1SkRhFbgJFck%2Fy77KtEg%3D&reserved=0>, \
docs<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fperk-software.cs. \
queensu.ca%2Fplus%2Fdoc%2Fnightly%2Fdev%2FvtkPlusMetaImageSequenceIO_8h.html&data=02%7 \
C01%7Classo%40queensu.ca%7C5a34db5cc49149f2b77b08d5c66b8a59%7Cd61ecb3b38b142d582c4efb2 \
838b925c%7C1%7C0%7C636633087559034726&sdata=NtNk%2Ftz712R0RIsO8YXlff2ds16C%2BVpZtgZpKWiCu3k%3D&reserved=0>). \
You might be able to use it directly.
Regards,
Dženan
On Wed, May 30, 2018 at 2:53 PM Andrew Harris <aharr8@uwo.ca<mailto:aharr8@uwo.ca>> \
wrote: Hello, I was wondering if it is possible to store additional information about \
an image as part of an MHA file. Specifically, we are capturing ultrasound using an \
arm that has encoders attached that report position in space, and I'd like to be able \
to include that information in the MHA file rather than keeping a separate record. \
Thanks in advance for the help.
--
AH
Andrew Harris, BSc with Honours (Medical Physics)
PhD (CAMPEP) & MClSc Candidate
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<div class="WordSection1">
<p class="MsoNormal"><span \
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Yes, \
Plus toolkit has been using mha and nrrd files for many years to store tracked \
ultrasound data in a single file. Recently we use nrrd format more, as this format \
supports 3D+t image sequences more cleanly. At the beginning, we used ITK's \
reader/writer, but metadata handling was not fast enough and we also needed dynamic \
header construction and memory-cached compressed streaming image I/O. We are now also \
adding support for lossy video codecs as non-standard \
extensions.<o:p></o:p></span></p> <p class="MsoNormal"><span \
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span \
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Plus \
can reconstruct volumes from tracked ultrasound slices, connect to many ultrasound \
devices through native interfaces, connect to most optical and electromagnetic \
trackers, stream tracked ultrasound data through OpenIGTLink for real-time \
visualization to various applications, perform spatial and temporal calibrations, \
etc. Check out <a href="http://www.plustoolkit.org">www.plustoolkit.org</a> and <a \
href="http://www.slicerigt.org"> www.slicerigt.org</a> for details. There is a \
resident Plus expert at Robarts, Adam Rankin, you can contact him if you need more \
information, and we'll have a one-week hackathon at Robarts in July where you can \
meet several experienced Plus and SlicerIGT users and developers (<a \
href="https://na-mic.github.io/ProjectWeek/PW29_2018_London_Canada/">https://na-mic.github.io/ProjectWeek/PW29_2018_London_Canada/</a>).<o:p></o:p></span></p>
<p class="MsoNormal"><span \
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span \
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Andras<o:p></o:p></span></p>
<p class="MsoNormal"><span \
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span \
style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span \
style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Community \
<community-bounces@itk.org> <b>On Behalf Of </b>Dženan Zukic<br>
<b>Sent:</b> Wednesday, May 30, 2018 4:26 PM<br>
<b>To:</b> Andrew Harris <aharr8@uwo.ca><br>
<b>Cc:</b> Insight-users <insight-users@itk.org><br>
<b>Subject:</b> Re: [ITK] [ITK-users] using MHA file to store additional information \
about image<o:p></o:p></span></p> <p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal"><span style="font-family:"Verdana",sans-serif">Hi \
Andrew,<o:p></o:p></span></p> </div>
<div>
<p class="MsoNormal"><span \
style="font-family:"Verdana",sans-serif"><o:p> </o:p></span></p> \
</div> <div>
<p class="MsoNormal"><span style="font-family:"Verdana",sans-serif">you can \
add content to image's MetaData dictionary. But you should look at how Plus does it \
(<a href="https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com% \
2FPlusToolkit%2FPlusLib%2Fblob%2Fmaster%2Fsrc%2FPlusCommon%2FIO%2FvtkPlusMetaImageSequ \
enceIO.cxx&data=02%7C01%7Classo%40queensu.ca%7C5a34db5cc49149f2b77b08d5c66b8a59%7C \
d61ecb3b38b142d582c4efb2838b925c%7C1%7C0%7C636633087559034726&sdata=9JCBbDgxqHogvLhKlhy8Vnk1SkRhFbgJFck%2Fy77KtEg%3D&reserved=0">code</a>, <a \
href="https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fperk-software.cs \
.queensu.ca%2Fplus%2Fdoc%2Fnightly%2Fdev%2FvtkPlusMetaImageSequenceIO_8h.html&data \
=02%7C01%7Classo%40queensu.ca%7C5a34db5cc49149f2b77b08d5c66b8a59%7Cd61ecb3b38b142d582c \
4efb2838b925c%7C1%7C0%7C636633087559034726&sdata=NtNk%2Ftz712R0RIsO8YXlff2ds16C%2BVpZtgZpKWiCu3k%3D&reserved=0">docs</a>).
You might be able to use it directly.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span \
style="font-family:"Verdana",sans-serif"><o:p> </o:p></span></p> \
</div> <div>
<p class="MsoNormal"><span \
style="font-family:"Verdana",sans-serif">Regards,<o:p></o:p></span></p> \
</div> <div>
<p class="MsoNormal"><span \
style="font-family:"Verdana",sans-serif">Dženan<o:p></o:p></span></p> \
</div> </div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">On Wed, May 30, 2018 at 2:53 PM Andrew Harris <<a \
href="mailto:aharr8@uwo.ca">aharr8@uwo.ca</a>> wrote:<o:p></o:p></p> </div>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0in 0in 0in \
6.0pt;margin-left:4.8pt;margin-right:0in"> <div>
<p class="MsoNormal">Hello, I was wondering if it is possible to store additional \
information about an image as part of an MHA file. Specifically, we are \
capturing ultrasound using an arm that has encoders attached that report position in \
space, and I'd like to be able to include that information in the MHA file rather \
than keeping a separate record. Thanks in advance for the help.<br clear="all"> \
<o:p></o:p></p> <div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p style="margin:0in;margin-bottom:.0001pt"><span \
style="font-family:"Arial",sans-serif;color:#232323">--<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span \
style="font-family:"Arial",sans-serif;color:#232323">AH<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt;min-height:15px"><span \
style="font-family:"Arial",sans-serif;color:#232323"><o:p> </o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><span \
style="font-family:"Arial",sans-serif;color:#232323">Andrew Harris, BSc \
with Honours (Medical Physics)<o:p></o:p></span></p> <p \
style="margin:0in;margin-bottom:.0001pt"><span \
style="font-family:"Arial",sans-serif;color:#232323">PhD (CAMPEP) & \
MClSc Candidate<o:p></o:p></span></p> <p \
style="margin:0in;margin-bottom:.0001pt"><span \
style="font-family:"Arial",sans-serif;color:#232323">----------------------- \
------------------------------------------------------------------------<o:p></o:p></span></p>
<p style="margin:0in;margin-bottom:.0001pt"><i><span \
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or distribution of this email (or any attachments thereto) by other than the \
intended recipient is strictly prohibited. If you are not the intended \
recipient, please contact the sender immediately and permanently destroy this \
email and any attachments thereto.</span></i><span \
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