[Insight-users] DICOM series

[Miller, James V (Research)]

If the filenames correspond to the image numbers, i.e. filenames like
IM100, IM101, etc so that 

IM100: location 1, time 1
IM101: location 1, time 2
IM102: location 1, time 3
...
IM10x: location 2, time 1
...
...

then  you could use the NumericSeriesFileNames to generate filenames
that can be passed to the ImageSeriesReader.  The NumericSeriesFileNames
takes a start index and a increment and a file pattern.  This would 
allow you to collect every Nth image into a series.

I wonder why there isn't a DICOM tag to identify the timestep uniquely.

Jim



-----Original Message-----
From: Uday Kurkure [mailto:udaykurkure at yahoo.com]
Sent: Thursday, October 21, 2004 1:42 PM
To: Miller, James V (Research); insight-users at itk.org
Subject: RE: [Insight-users] DICOM series



Hello James,

You were right. The Instance UIDs (and Image Numbers
too) are 0 for all the secondary captures. So, I would
prefer to sort the primary captures. About time tags,
I know of two:

Acquisition time: 0008,0032 - The time the acquisition
of data for the image started.

Image time: 0008,0033 - The time the image pixel
creation started.

But these tags are same for all the images in a
series.  So they are of no help to me.

When I sort a series by image number the data has the
order: 
location L1, time T1
location L1, time T2
...
location L1, time TN
...
location L2, time T1
location L2, time T2
...
location L2, time TN
...
...
location LM, time TN
so on.

So one thing I can think of is to have user input M
(number of slices in a volume) and N (number of
phases), and group the slices in N groups 

- taking every Nth slice in one group - OPTION : EVERY
N PHASE

- For data where the slices are ordered location wise
first, we can just group first N slices in first group
and so on - OPTION: DEFAULT

Do you think its possible? If yes, how can I do it in
ITK? 

Thanks,

Uday
















--- "Miller, James V (Research)" <millerjv at crd.ge.com>
wrote:

> Uday, 
> 
> Do you know what DICOM tag distinguishes the time
> instants? We can add
> the ability to the DICOM code to group based on
> time.
> 
> I have seen the second issue before. Can you check
> the Instance 
> UIDs (0x0008, 0x0018) for each of the images in the
> new folder?  
> 
> You can use DICOMWorks (free download) to look at
> the DICOM tags.  
> I have seen secondary captures use the same Instance
> UID for each image 
> (say 0.0.0.0).  The UIDs are supposed to be unique
> on an image to 
> image basis.  The DICOM code in ITK uses the  UID's
> as keys in several 
> maps.  If the UIDs are not unique, the a single file
> gets read for each 
> slice in the volume. The short term fix is to fix
> the UIDs in the DICOM
> files.  DICOMWorks allows you to do this as well.
> 
> Check the DICOM tags (0x0008, 0x0018) to see if the
> field is unique across
> all your images.
> 
> Jim
> 
> 
> 
> -----Original Message-----
> From: Uday Kurkure [mailto:udaykurkure at yahoo.com]
> Sent: Wednesday, October 20, 2004 6:26 PM
> To: insight-users at itk.org
> Subject: [Insight-users] DICOM series
> 
> 
> 
> 
> Hello all,
> 
> I have been playing with ITK DICOM series image
> read/write and MRIconvert to write a volume image in
> .raw format. The findings and problems:
> 
> 1. In a single series there are slices of volumes
> acquired at different time instants. And
> unfortunately, the acquisition time label in the
> headers is same for all. So, sorting by slice
> location
> doesn't work properly as there are more than one
> slices at the same position (of different time
> instants). Is there any other way to sort the slices
> in a volume and also sort the volumes?
> (These are original primary capture images)
> 
> 2. I myself sorted the images for one volume
> (acquired
> at one time instant)and saved them in a separate
> folder with naming convention: 
> msPP_VV_SS.dcm, where PP is subject number, VV is
> volume number and SS is the slice number in that
> volume. But now also if I run the code, it reads a
> single slice 'ms01_01_05.dcm' 11 times (there are 11
> slices in the folder). How to fix this? (Since this
> is
> secondary write of DICOM images, Image Number info
> is
> lost, but rest all (like slice location, patient
> position/orientation etc) are there in the header.
> 
> Thanks,
> 
> -Uday
> 
> 
> 
> 
> 
> 
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