[Insight-users] Problem with Analyze format

Tue, 20 Jan 2004 11:11:14 -0800

This message is in MIME format. Since your mail reader does not understand
this format, some or all of this message may not be legible.

------_=_NextPart_001_01C3DF88.D032D266
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Hi Benjamin,
Thanks for the suggestions. I just now, followed the suggestion of =
Vince (Dr
Vincent A. Magnotta) and when writing out the images, I set it to =
signed
integer. This appears to solve the problem. I think this is because, =
Analyze
writes in signed format and when we set the output type to unsigned, =
that
mixes up the header information.

Radhika

-----Original Message-----
From: Benjamin King [mailto:king.benjamin at mh-hannover.de]=20
Sent: Monday, January 19, 2004 4:51 AM
To: Radhika Sivaramakrishna; ITK
Subject: Re: [Insight-users] Problem with Analyze format

Hi Radhika,

> There appears to be a problem with the Analyze format. When I read in =
an
> unsigned 16 bit integer data, and write it out in Analyze format, the =

> header that goes with the .img file appears incompatible so I cannot=20
> view it

I experience a similar behaviour when I try to open ITK's Analyze files =
in=20
e.g. VolView. I fix the header by first opening the file with MRIcro=20
(http://www.psychology.nottingham.ac.uk/staff/cr1/mricro.html). Then in =

the Header->Information dialog, set the field G_Max to something other=20
than 0, e.g. 4095 (which is the maximum for 12bit unsigned int data).=20
Finally save the header overwriting the old one. VolView can now read =
and=20
display the file.

For another software package, I also have to change the scale field (on =

the MRIcro main window just below the endianess display) to something=20
greater than 0.

If you'd like to know more about the Analyze format, you may refer to=20
http://www.dclunie.com/medical-image-faq/html/part5.html or=20
http://www.mayo.edu/bir/PDF/ANALYZE75.pdf

cheers,
   Benjamin

--=20
Benjamin King
Institut f=FCr Medizinische Informatik
Medizinische Hochschule Hannover
Tel.: +49  511  532-2663
                                                    =20
----------------------------------------------------- =20
Confidentiality Notice.=20
This email message is for the sole use of the intended recipient(s) and =
may
contain confidential and privileged information. Any unauthorized =
review,
use, disclosure or distribution is prohibited. If you are not the =
intended
recipient, please contact the sender by reply email and destroy all =
copies
of the original message. If you are the intended recipient, please be
advised that the content of this message is subject to access, review =
and
disclosure by the sender's Email System Administrator.

------_=_NextPart_001_01C3DF88.D032D266
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2//EN">
<HTML>
<HEAD>
<META HTTP-EQUIV=3D"Content-Type" CONTENT=3D"text/html; =
charset=3Diso-8859-1">
<META NAME=3D"Generator" CONTENT=3D"MS Exchange Server version =
5.5.2656.87">
<TITLE>RE: [Insight-users] Problem with Analyze format</TITLE>
</HEAD>
<BODY>

Hi Benjamin,
 Thanks for the suggestions. I just now, followed the =
suggestion of Vince (Dr Vincent A. Magnotta) and when writing out the =
images, I set it to signed integer. This appears to solve the problem. =
I think this is because, Analyze writes in signed format and when we =
set the output type to unsigned, that mixes up the header =
information.

<P><FONT SIZE=3D2>Radhika</FONT>
</P>

<P><FONT SIZE=3D2>-----Original Message-----</FONT>
<BR><FONT SIZE=3D2>From: Benjamin King [<A =
HREF=3D"mailto:king.benjamin at mh-hannover.de">mailto:king.benjamin at mh-han=
nover.de</A>] </FONT>
<BR><FONT SIZE=3D2>Sent: Monday, January 19, 2004 4:51 AM</FONT>
<BR><FONT SIZE=3D2>To: Radhika Sivaramakrishna; ITK</FONT>
<BR><FONT SIZE=3D2>Subject: Re: [Insight-users] Problem with Analyze =
format</FONT>
</P>

<P><FONT SIZE=3D2>Hi Radhika,</FONT>
</P>
<BR>

&gt; There appears to be a problem with the Analyze =
format. When I read in an
 &gt; unsigned 16 bit integer data, and write it out =
in Analyze format, the 
 &gt; header that goes with the .img file appears =
incompatible so I cannot 
 &gt; view it

I experience a similar behaviour when I try to open =
ITK's Analyze files in 
 e.g. VolView. I fix the header by first opening the =
file with MRIcro 
 (<A =
HREF=3D"http://www.psychology.nottingham.ac.uk/staff/cr1/mricro.html" =
TARGET=3D"_blank">http://www.psychology.nottingham.ac.uk/staff/cr1/mricr=
o.html</A>). Then in 
 the Header-&gt;Information dialog, set the field =
G_Max to something other 
 than 0, e.g. 4095 (which is the maximum for 12bit =
unsigned int data). 
 Finally save the header overwriting the old one. =
VolView can now read and 
 display the file.

<P><FONT SIZE=3D2>For another software package, I also have to change =
the scale field (on </FONT>
<BR><FONT SIZE=3D2>the MRIcro main window just below the endianess =
display) to something </FONT>
<BR><FONT SIZE=3D2>greater than 0.</FONT>
</P>

<P><FONT SIZE=3D2>If you'd like to know more about the Analyze format, =
you may refer to </FONT>
<BR><FONT SIZE=3D2><A =
HREF=3D"http://www.dclunie.com/medical-image-faq/html/part5.html" =
TARGET=3D"_blank">http://www.dclunie.com/medical-image-faq/html/part5.ht=
ml</A> or </FONT>
<BR><FONT SIZE=3D2><A =
HREF=3D"http://www.mayo.edu/bir/PDF/ANALYZE75.pdf" =
TARGET=3D"_blank">http://www.mayo.edu/bir/PDF/ANALYZE75.pdf</A></FONT>
</P>
<BR>

<P><FONT SIZE=3D2>cheers,</FONT>
<BR><FONT SIZE=3D2>&nbsp;&nbsp; Benjamin</FONT>
</P>

-- 
 Benjamin King
 Institut f=FCr Medizinische Informatik
 Medizinische Hochschule Hannover
 Tel.: +49&nbsp; 511&nbsp; 532-2663
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 
 -----------------------------------------------------&nbsp; =

 Confidentiality Notice. 
 This email message is for the sole use of the =
intended recipient(s) and may contain confidential and privileged =
information. Any unauthorized review, use, disclosure or distribution =
is prohibited. If you are not the intended recipient, please contact =
the sender by reply email and destroy all copies of the original =
message. If you are the intended recipient, please be advised that the =
content of this message is subject to access, review and disclosure by =
the sender's Email System Administrator.

</BODY>
</HTML>
------_=_NextPart_001_01C3DF88.D032D266--