[Insight-users] reading 512x 512 ct dicom images
Miller, James V (Research)
millerjv at crd.ge.com
Tue, 27 Apr 2004 11:29:51 -0400
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We read full CT image series with the DICOMSeriesFilenames all the time. If
the directory contains multiple image series, then the DICOMSeriesFilenames
will return the images in the first series it finds (by default). The first
series in a directory is frequently a scout series and not what you what to
process. However, you can tell the DICOMSeriesFilenames to get the
filenames for a particular series (specified by UID).
The size of the images is determined from the DICOM headers.
If you run the DicomSeriesReadImageWriter example specifying a directory of
DICOM files, it will list all the series UIDs in the that directory (and
read the first series it finds by default). Then you can run the example a
second time specifying the series UID that you want. We could probably
change the example to have an option to just list the series UIDs and the
number of files in each series (without reading the first series by
default).
If none of this information helps you solve your problem, then we'll need a
couple of the DICOM CT images to track down the problem. We probably do not
need the entire volume, just 2 or 3 slices from the series you want. You
can send them to me.
Jim
-----Original Message-----
From: raghu venkatram [mailto:raghu_420 at hotmail.com]
Sent: Tuesday, April 27, 2004 10:05 AM
To: luis.ibanez at kitware.com
Cc: insight-users at itk.org
Subject: Re: [Insight-users] reading 512x 512 ct dicom images
hello Luis,
Using the dicom series reader example, and trying to read 512 x 512 ct
images. I tried using a directory that contained multiple series and also
just one. In both cases only the first 2 slices are read. There is not
"crash", the program terminates.
I set up the example so that I read my dicom images and write them at in
Analyze format. using 256 x 256 MR slices, my analyze image contains all the
slices.
I also tried getting the spacing information, I get the right spacing for
the MR volume as in its header, while i get 1,1,1 for the CT slices. I
double checked to make sure i wasnt doing something silly.
Apart from this, I have used MRICro to convert my MR and CT volumes into
Analyze format, and my ITK registration application works just fine. So I
thought instead of converting why not just use DICOM as is through ITK and
ran into the CT reading problem.
A colleague of mine, says he had to change hard coded image height and width
from 256 to 512 in one of the itk files, which i dont believe is right as
this information in all fairness must be dynamically obtained from the image
header. I could give you my ct volume, if you would like to test them out.
Also please tell me that the image dimensions are not hardcoded.
Thank you,
Raghu
>From: Luis Ibanez <luis.ibanez at kitware.com>
>To: raghu venkatram <raghu_420 at hotmail.com>
>CC: insight-users at itk.org
>Subject: Re: [Insight-users] reading 512x 512 ct dicom images
>Date: Mon, 26 Apr 2004 13:10:03 -0400
>
>
>Hi Raghu,
>
>In the case of the CT images that only write 2 slices...
>
>Could you please be more specific regarding the action
>of the executable:
>
>You said:
>
> 1) It crashes
> 2) The name generator gives all the dicom files
> 3) When you write the volume only 2 slices appear
>
>Maybe you could post the text output from the program
>so we can see the order in which things happened.
>Crashes is a very generic term. It could have been a
>segmentation fault, a catched exception or an uncatched
>exception... Again, if you post the text output of the
>program, that will help us to figure out what is happening.
>
>
> Thanks,
>
>
> Luis
>
>
>
>----------------------
>raghu venkatram wrote:
>
>>hi Luis,
>> I have looked at teh dicomseriesreader example. and while using
>>the example, and trying to write out my ct volume, it crashes, the
>>name generator gives me all the names of the dicom files in the
>>directory, but when i write it out it writes out only 2 slices.
>> I have tried the the same program with a 256 x 256 mr volume, and
>>i am able to write it out. Now i am able to read both my MR and CT
>>volumes using MRICro and AMIDE with no problems, also i am able to
>>convert them into ANALYZE format using MRICro and use it in my ITK
>>program.
>> Also when i try getting the spacing information of my CT volume
>>after reading the image, i get 1,1,1 instad of .5 .5 2, but i get
>>the right spacing information for my MR volume using the
>>dicomseriesreader example.
>> please also not that MRICro and AMIDE both give the rght spacing
>>for both CT and MR volumes and the right spacing.
>> Thanks for the continued support
>>Raghu
>>
>>
>
>
>
>_______________________________________________
>Insight-users mailing list
>Insight-users at itk.org
>http://www.itk.org/mailman/listinfo/insight-users
_____
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_______________________________________________ Insight-users mailing list
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<DIV><SPAN class=183330115-27042004><FONT color=#0000ff size=2>We read full CT
image series with the DICOMSeriesFilenames all the time. If the directory
contains multiple image series, then the DICOMSeriesFilenames will return the
images in the first series it finds (by default). The first series in a
directory is frequently a scout series and not what you what to process.
However, you can tell the DICOMSeriesFilenames to get the filenames for a
particular series (specified by UID).</FONT></SPAN></DIV>
<DIV><SPAN class=183330115-27042004><FONT color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=183330115-27042004><FONT color=#0000ff size=2>The size of the
images is determined from the DICOM headers.</FONT></SPAN></DIV>
<DIV><SPAN class=183330115-27042004><FONT color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=183330115-27042004><FONT color=#0000ff size=2>If you run the
DicomSeriesReadImageWriter example specifying a directory of DICOM files, it
will list all the series UIDs in the that directory (and read the first series
it finds by default). Then you can run the example a second time specifying the
series UID that you want. We could probably change the example to have an option
to just list the series UIDs and the number of files in each series (without
reading the first series by default).</FONT></SPAN></DIV>
<DIV><SPAN class=183330115-27042004><FONT color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=183330115-27042004><FONT color=#0000ff size=2>If none of this
information helps you solve your problem, then we'll need a couple of the DICOM
CT images to track down the problem. We probably do not need the entire
volume, just 2 or 3 slices from the series you want. You can send them to
me.</FONT></SPAN></DIV>
<DIV><SPAN class=183330115-27042004><FONT color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=183330115-27042004><FONT color=#0000ff
size=2>Jim</FONT></SPAN></DIV>
<DIV><SPAN class=183330115-27042004><FONT color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=183330115-27042004><FONT color=#0000ff
size=2></FONT></SPAN> </DIV>
<BLOCKQUOTE>
<DIV class=OutlookMessageHeader dir=ltr align=left><FONT face=Tahoma
size=2>-----Original Message-----<BR><B>From:</B> raghu venkatram
[mailto:raghu_420 at hotmail.com]<BR><B>Sent:</B> Tuesday, April 27, 2004 10:05
AM<BR><B>To:</B> luis.ibanez at kitware.com<BR><B>Cc:</B>
insight-users at itk.org<BR><B>Subject:</B> Re: [Insight-users] reading 512x 512
ct dicom images<BR><BR></FONT></DIV>
<DIV>
<DIV class=RTE>
<P>hello Luis,</P>
<P>Using the dicom series reader example, and trying to read 512 x 512 ct
images. I tried using a directory that contained multiple series and also just
one. In both cases only the first 2 slices are read. There is not "crash", the
program terminates.</P>
<P>I set up the example so that I read my dicom images and write them at in
Analyze format. using 256 x 256 MR slices, my analyze image contains all the
slices.</P>
<P>I also tried getting the spacing information, I get the right spacing for
the MR volume as in its header, while i get 1,1,1 for the CT slices. I double
checked to make sure i wasnt doing something silly. </P>
<P>Apart from this, I have used MRICro to convert my MR and CT volumes into
Analyze format, and my ITK registration application works just fine. So I
thought instead of converting why not just use DICOM as is through ITK and ran
into the CT reading problem.</P>
<P>A colleague of mine, says he had to change hard coded image height and
width from 256 to 512 in one of the itk files, which i dont believe is right
as this information in all fairness must be dynamically obtained from the
image header. I could give you my ct volume, if you would like to test them
out. Also please tell me that the image dimensions are not hardcoded.</P>
<P>Thank you,</P>
<P>Raghu<BR><BR></P></DIV>
<DIV></DIV>>From: Luis Ibanez <luis.ibanez at kitware.com>
<DIV></DIV>>To: raghu venkatram <raghu_420 at hotmail.com>
<DIV></DIV>>CC: insight-users at itk.org
<DIV></DIV>>Subject: Re: [Insight-users] reading 512x 512 ct dicom images
<DIV></DIV>>Date: Mon, 26 Apr 2004 13:10:03 -0400
<DIV></DIV>>
<DIV></DIV>>
<DIV></DIV>>Hi Raghu,
<DIV></DIV>>
<DIV></DIV>>In the case of the CT images that only write 2 slices...
<DIV></DIV>>
<DIV></DIV>>Could you please be more specific regarding the action
<DIV></DIV>>of the executable:
<DIV></DIV>>
<DIV></DIV>>You said:
<DIV></DIV>>
<DIV></DIV>> 1) It crashes
<DIV></DIV>> 2) The name generator gives all the
dicom files
<DIV></DIV>> 3) When you write the volume only 2
slices appear
<DIV></DIV>>
<DIV></DIV>>Maybe you could post the text output from the program
<DIV></DIV>>so we can see the order in which things happened.
<DIV></DIV>>Crashes is a very generic term. It could have been a
<DIV></DIV>>segmentation fault, a catched exception or an uncatched
<DIV></DIV>>exception... Again, if you post the text output of the
<DIV></DIV>>program, that will help us to figure out what is happening.
<DIV></DIV>>
<DIV></DIV>>
<DIV></DIV>> Thanks,
<DIV></DIV>>
<DIV></DIV>>
<DIV></DIV>> Luis
<DIV></DIV>>
<DIV></DIV>>
<DIV></DIV>>
<DIV></DIV>>----------------------
<DIV></DIV>>raghu venkatram wrote:
<DIV></DIV>>
<DIV></DIV>>>hi Luis,
<DIV></DIV>>> I have looked at teh dicomseriesreader example.
and while using
<DIV></DIV>>>the example, and trying to write out my ct volume, it
crashes, the
<DIV></DIV>>>name generator gives me all the names of the dicom files in
the
<DIV></DIV>>>directory, but when i write it out it writes out only 2
slices.
<DIV></DIV>>> I have tried the the same program with a 256 x
256 mr volume, and
<DIV></DIV>>>i am able to write it out. Now i am able to read both my MR
and CT
<DIV></DIV>>>volumes using MRICro and AMIDE with no problems, also i am
able to
<DIV></DIV>>>convert them into ANALYZE format using MRICro and use it in
my ITK
<DIV></DIV>>>program.
<DIV></DIV>>> Also when i try getting the spacing information
of my CT volume
<DIV></DIV>>>after reading the image, i get 1,1,1 instad of .5 .5 2, but
i get
<DIV></DIV>>>the right spacing information for my MR volume using the
<DIV></DIV>>>dicomseriesreader example.
<DIV></DIV>>> please also not that MRICro and AMIDE both give
the rght spacing
<DIV></DIV>>>for both CT and MR volumes and the right spacing.
<DIV></DIV>>> Thanks for the continued support
<DIV></DIV>>>Raghu
<DIV></DIV>>>
<DIV></DIV>>>
<DIV></DIV>>
<DIV></DIV>>
<DIV></DIV>>
<DIV></DIV>>_______________________________________________
<DIV></DIV>>Insight-users mailing list
<DIV></DIV>>Insight-users at itk.org
<DIV></DIV>>http://www.itk.org/mailman/listinfo/insight-users
<DIV></DIV></DIV><BR clear=all>
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