[Insight-users] Slice order comes wrong when reading a DICOM files (one slice per file) to form a volume

[Desikachari Nadadur]

Hi again,

Just to clarify: On FreeBSD, I could make the file ordering on the disk 
to be same as the slice ordering, by copying the files one by one in 
order to a different directory. However, that does not work on Debian 
Linux because the ext2 file system maintain a hash for filename 
ordering. This issue therefore is not really OS dependent but file 
system dependent (UFS vs. ext2). I just want to use the DICOM tags for 
getting correct slice ordering so that this file system dependency is 
eliminated.

Thanks in advance for any suggestions you may have.

Desika

--
Desikachari Nadadur, PhD
INTIO, Inc.

Desikachari Nadadur wrote:
> Hi All,
>
> I searched the forum but I could not find any answer to my question. 
> So, I am posting here.
>
> When reading a set of CT DICOM files (with one file per slice) to form 
> a volume, the slice ordering comes out wrong for some datasets. This 
> also seems system dependent. For example the same dataset works on 
> FreeBSD 8.0 and fails on Debian (Stable) Linux. Here "fails" means 
> wrong order of slices. Also, the ordering seems to coincide with the 
> filename ordering on the disk in these failed cases. When I do "ls -f" 
> on these systems, FreeBSD 8.0 shows all the files with disk ordering 
> coinciding with volume's slice ordering. However, on Debian Linux, it 
> is not the case. 99% of the time I am able to successfully read the 
> datasets even if the file ordering on the disk is not the volume slice 
> ordering. Looks like I am not using a much needed DICOM tag in getting 
> the slice ordering correct. Here is the code segment where I call 
> AddSeriesRestriction () to set the tags to base sorting upon while 
> reading the series of files. There is no sorting based on 
> InstanceNumber and I did not know how to implement it here. I am using 
> ITK 3.14.0 with GDCM 2.0.12.  Any suggestions to fix this problem 
> would be appreciated.
>
> <CODE>
>        ITKNamesGeneratorType :: Pointer nameGenerator = 
> ITKNamesGeneratorType :: 
> New();                                                                                                       
>
>        nameGenerator->SetUseSeriesDetails( true );
>                                                                                                        
>
>        // We want to add two more criteria for sorting 
> filenames                                             //  * 
> 0008|0021   Series 
> Date                                                                  
>        //  * 0020|0012   Acquisition 
> Number                                                           
>        // using the call to 
> AddSeriesRestriction()                                                    
>        
> //                                                                                              
>
>        nameGenerator->AddSeriesRestriction( "0008|0021" ); // DA 1 
> Series Date                               
> nameGenerator->AddSeriesRestriction( "0020|0012" ); // Acquisition 
> Number                      
>                                                                                                        
>
>        nameGenerator->SetDirectory( filename 
> );                                                       
>                                                                                                        
>
>        typedef std :: vector< std :: string >    
> SeriesIdContainer;                                      const 
> SeriesIdContainer & seriesUID = 
> nameGenerator->GetSeriesUIDs();                      
>                                                                                                        
>                                                                                                       
>
>        std :: string 
> seriesIdentifier;                                                             
>
>        seriesIdentifier = seriesUID.begin()->c_str();
>
>        typedef std :: vector< std :: string >   
> FileNamesContainer;                                      
> FileNamesContainer 
> fileNames;                                                              
>        fileNames = nameGenerator->GetFileNames( seriesIdentifier 
> );                               
>                                                                                                        
>
>        class ITKSeriesReaderType :: Pointer itkReader = 
> ITKSeriesReaderType :: New();              
>                                                                                                       
>
>        itkReader->SetImageIO( itkGdcmImageIO 
> );                                                    
>                                                                                                       
>
>        itkReader->SetFileNames( fileNames 
> );                                                      
>                                                                                                        
>
>        
> itkReader->Update();                                                                    
>
> </CODE>
>
> Thanks in advance,
> Desika
>
> -- 
> Desikachari Nadadur, PhD
> INTIO, Inc.
>
>