[Insight-users] Proton Density/T2-weighted images
Radhika Sivaramakrishna
radhika.sivaramakrishna at synarc.com
Fri, 9 Jan 2004 10:33:03 -0800
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Hi Luis,
I want to create a new DicomSeriesFileNames which can sort based on Echo
time (which is the basic differentiator to separate PD from T2). I checked
the .txx file and .h for DicomSeriesFileNames and saw the switch for sorting
by image number, image position and slice location. However, I don't see an
obvious way of adding in the check for things like Echo time. How do I do
this?
Thanks
Radhika
-----Original Message-----
From: Luis Ibanez [mailto:luis.ibanez at kitware.com]
Sent: Monday, January 05, 2004 1:38 PM
To: Radhika Sivaramakrishna
Cc: 'insight-users at itk.org'
Subject: Re: [Insight-users] Proton Density/T2-weighted images
Hi Radhika,
About your questions:
1) This sounds like a byte swapping problem. It is likely that you are
moving
data from a platform with big-endian architecture to another one with
little-endian architecture.
What format are your original images on ?
If you were using the MetaImage format, it is pretty easy to switch the
endianess by just changing the header entry ElementByteOrderMSB.
2) Yeap, the easy way is to use MRIConvert:
http://lcni.uoregon.edu/~jolinda/MRIConvert
from Jolinda Smith at the Lewis Center for Neuroimaging
<http://lcni.uoregon.edu/>
at the University of Oregon <http://www.uoregon.edu/>.
Read your series using this application and identify the
DICOM fields that differentiate your T2 from PD datasets.
Once you identify the fields, you can use this information
for creating a new DICOMSeriesFileNames class (of
course named differently).
Note also that you can simply save the data from MRIConvert,
into Analyze or MetaImage format.
Regards,
Luis
------------------------------------
Radhika Sivaramakrishna wrote:
> Hi Luis,
>
> I have two questions:
>
>
>
> 1) I tried to use the code you had sent me previously to read a
> series image and save as Analyze format. Unfortunately although the
> original images are of type which can definitely be supported by
> unsigned short, the output image looks totally scrambled up. If I
> change pixel type to unsigned char, then the image looks okay but I
> lose all the high values and that's obviously visible. Could you tell
> me what the problem might be?
>
> 2) I have a large number of double spin echo images where the
> shorter echo is PD and larger is T2-weighted. I want to extract only
> the T2-weighted. They are part of the same series. I know that in the
> software guide you have used a lot of PD/T2-weighted examples, so
> there must be a way to extract this. With DicomSeriesFileName I see
> that you can sort by ImageNumber, Image Position or Slice Location.
> Unfortunately none of these will help sort T2 from PD. Is there a
> better way to do this?
>
>
>
> Thanks
>
> Radhika
>
>
>
> -----------------------------------------------------
>
> Confidentiality Notice.
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<P><FONT SIZE=3D2>Hi Luis,</FONT>
<BR><FONT SIZE=3D2>I want to create a new DicomSeriesFileNames which =
can sort based on Echo time (which is the basic differentiator to =
separate PD from T2). I checked the .txx file and .h for =
DicomSeriesFileNames and saw the switch for sorting by image number, =
image position and slice location. However, I don't see an obvious way =
of adding in the check for things like Echo time. How do I do =
this?</FONT></P>
<P><FONT SIZE=3D2>Thanks</FONT>
<BR><FONT SIZE=3D2>Radhika</FONT>
</P>
<BR>
<P><FONT SIZE=3D2>-----Original Message-----</FONT>
<BR><FONT SIZE=3D2>From: Luis Ibanez [<A =
HREF=3D"mailto:luis.ibanez at kitware.com">mailto:luis.ibanez at kitware.com</=
A>] </FONT>
<BR><FONT SIZE=3D2>Sent: Monday, January 05, 2004 1:38 PM</FONT>
<BR><FONT SIZE=3D2>To: Radhika Sivaramakrishna</FONT>
<BR><FONT SIZE=3D2>Cc: 'insight-users at itk.org'</FONT>
<BR><FONT SIZE=3D2>Subject: Re: [Insight-users] Proton =
Density/T2-weighted images</FONT>
</P>
<P><FONT SIZE=3D2>Hi Radhika,</FONT>
</P>
<P><FONT SIZE=3D2>About your questions:</FONT>
</P>
<P><FONT SIZE=3D2>1) This sounds like a byte swapping problem. It =
is likely that you are </FONT>
<BR><FONT SIZE=3D2>moving</FONT>
<BR><FONT SIZE=3D2> data from a platform with =
big-endian architecture to another one with</FONT>
<BR><FONT SIZE=3D2> little-endian =
architecture.</FONT>
</P>
<P><FONT SIZE=3D2> What format are your =
original images on ?</FONT>
</P>
<P><FONT SIZE=3D2> If you were using the MetaImage =
format, it is pretty easy to switch the</FONT>
<BR><FONT SIZE=3D2> endianess by just changing the =
header entry ElementByteOrderMSB.</FONT>
</P>
<BR>
<P><FONT SIZE=3D2>2) Yeap, the easy way is to use MRIConvert:</FONT>
</P>
<P><FONT =
SIZE=3D2> &nb=
sp; <A HREF=3D"http://lcni.uoregon.edu/~jolinda/MRIConvert" =
TARGET=3D"_blank">http://lcni.uoregon.edu/~jolinda/MRIConvert</A></FONT>=
</P>
<BR>
<P><FONT SIZE=3D2> from Jolinda Smith at the Lewis Center =
for Neuroimaging </FONT>
<BR><FONT SIZE=3D2><<A HREF=3D"http://lcni.uoregon.edu/" =
TARGET=3D"_blank">http://lcni.uoregon.edu/</A>></FONT>
<BR><FONT SIZE=3D2> at the University of Oregon <<A =
HREF=3D"http://www.uoregon.edu/" =
TARGET=3D"_blank">http://www.uoregon.edu/</A>>.</FONT>
</P>
<BR>
<P><FONT SIZE=3D2> Read your series using this =
application and identify the</FONT>
<BR><FONT SIZE=3D2> DICOM fields that differentiate =
your T2 from PD datasets.</FONT>
<BR><FONT SIZE=3D2> </FONT>
<BR><FONT SIZE=3D2> Once you identify the fields, you =
can use this information</FONT>
<BR><FONT SIZE=3D2> for creating a new =
DICOMSeriesFileNames class (of</FONT>
<BR><FONT SIZE=3D2> course named =
differently).</FONT>
</P>
<P><FONT SIZE=3D2> Note also that you can simply save =
the data from MRIConvert,</FONT>
<BR><FONT SIZE=3D2> into Analyze or MetaImage =
format.</FONT>
</P>
<BR>
<P><FONT SIZE=3D2>Regards,</FONT>
</P>
<BR>
<P><FONT SIZE=3D2> Luis</FONT>
</P>
<P><FONT SIZE=3D2>------------------------------------</FONT>
<BR><FONT SIZE=3D2>Radhika Sivaramakrishna wrote:</FONT>
</P>
<P><FONT SIZE=3D2>> Hi Luis,</FONT>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>> I have two questions:</FONT>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>> 1) I tried =
to use the code you had sent me previously to read a </FONT>
<BR><FONT SIZE=3D2>> series image and save as Analyze format. =
Unfortunately although the </FONT>
<BR><FONT SIZE=3D2>> original images are of type which can =
definitely be supported by </FONT>
<BR><FONT SIZE=3D2>> unsigned short, the output image looks totally =
scrambled up. If I </FONT>
<BR><FONT SIZE=3D2>> change pixel type to unsigned char, then the =
image looks okay but I </FONT>
<BR><FONT SIZE=3D2>> lose all the high values and that's obviously =
visible. Could you tell </FONT>
<BR><FONT SIZE=3D2>> me what the problem might be?</FONT>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>> 2) I have a =
large number of double spin echo images where the </FONT>
<BR><FONT SIZE=3D2>> shorter echo is PD and larger is T2-weighted. I =
want to extract only </FONT>
<BR><FONT SIZE=3D2>> the T2-weighted. They are part of the same =
series. I know that in the </FONT>
<BR><FONT SIZE=3D2>> software guide you have used a lot of =
PD/T2-weighted examples, so </FONT>
<BR><FONT SIZE=3D2>> there must be a way to extract this. With =
DicomSeriesFileName I see </FONT>
<BR><FONT SIZE=3D2>> that you can sort by ImageNumber, Image =
Position or Slice Location. </FONT>
<BR><FONT SIZE=3D2>> Unfortunately none of these will help sort T2 =
from PD. Is there a </FONT>
<BR><FONT SIZE=3D2>> better way to do this?</FONT>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>> Thanks</FONT>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>> Radhika</FONT>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>> </FONT>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>> =
-----------------------------------------------------</FONT>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>> Confidentiality Notice.</FONT>
<BR><FONT SIZE=3D2>></FONT>
<BR><FONT SIZE=3D2>> This email message is for the sole use of the =
intended recipient(s) </FONT>
<BR><FONT SIZE=3D2>> and may contain confidential and privileged =
information. Any </FONT>
<BR><FONT SIZE=3D2>> unauthorized review, use, disclosure or =
distribution is prohibited. If </FONT>
<BR><FONT SIZE=3D2>> you are not the intended recipient, please =
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<BR><FONT SIZE=3D2>> email and destroy all copies of the original =
message. If you are the </FONT>
<BR><FONT SIZE=3D2>> intended recipient, please be advised that the =
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<BR><FONT SIZE=3D2>> is subject to access, review and disclosure by =
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<BR><FONT SIZE=3D2>> System Administrator.</FONT>
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<BR><FONT =
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<BR><FONT SIZE=3D2>Confidentiality Notice. </FONT>
<BR><FONT SIZE=3D2>This email message is for the sole use of the =
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