Question about reading 3rd party volume data

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Question about reading 3rd party volume data

Sarper Gürel
Hello people

I am quite new to the slicer. I have a question about importing data
from other visualization software. I have a 3d dataset from "VGI Max"
software and I want to use it on Slicer 3.4. The following header
information is available for the dataset (It is actually a big single
file)
        ----------------------
        {volume1}
        [representation]
        size = 383 383 420
        resamplemode = not activated
        datatype = unsigned integer
        datarange = 0 -1
        bitsperelement = 8
        [file1]
        RegionOfInterestStart = 0 0 0
        RegionOfInterestEnd = 382 382 419
        SkipHeader = 22
        FileFormat = raw
        Size = 383 383 420
        Mirror = 0 0 1
        Name = C:/mydata.dat
        Datatype = unsigned integer
        BitsPerElement = 8
        ----------------------

It tried several combination of properties in the Slicer module
"Volumes", but did not accomplished to see the data. Is Slicer capable
of reading this kind of file?

Thanks in advance and greets from Switzerland.

Sarper Gürel
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Re: Question about reading 3rd party volume data

pieper
Administrator
Hi Sarper -

Probably the easiest is to create a slicer-compatible header that points
to the data in your existing data file.  It looks like you have all the
needed info.

You could use a .nhdr file or a .mhd - see the info at the links below.

Best,
Steve

http://teem.sourceforge.net/nrrd/format.html

http://www.itk.org/Wiki/MetaIO


On J/11/10 3:57 AM, Sarper Gürel wrote:

> Hello people
>
> I am quite new to the slicer. I have a question about importing data
> from other visualization software. I have a 3d dataset from "VGI Max"
> software and I want to use it on Slicer 3.4. The following header
> information is available for the dataset (It is actually a big single
> file)
> ----------------------
> {volume1}
> [representation]
> size = 383 383 420
> resamplemode = not activated
> datatype = unsigned integer
> datarange = 0 -1
> bitsperelement = 8
> [file1]
> RegionOfInterestStart = 0 0 0
> RegionOfInterestEnd = 382 382 419
> SkipHeader = 22
> FileFormat = raw
> Size = 383 383 420
> Mirror = 0 0 1
> Name = C:/mydata.dat
> Datatype = unsigned integer
> BitsPerElement = 8
> ----------------------
>
> It tried several combination of properties in the Slicer module
> "Volumes", but did not accomplished to see the data. Is Slicer capable
> of reading this kind of file?
>
> Thanks in advance and greets from Switzerland.
>
> Sarper Gürel
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
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Re: Question about reading 3rd party volume data

Isaiah Norton
Hi Sarper,

Could you send your current nhdr with the next email? Maybe we'll spot
something with a quick look.

The error might be from a mismatch between number of dimensions expected
and files available. The nhdr should specify only three dimensions for
your data (because it is a single 3d file), and one hard (not magic)
file name. The header I sent is for quasi-4d data, so it expects
multiple sets of files. This is controlled by (at least) the tags:

dimensions, sizes, space directions, centers, kinds, data file

Are there any other errors before these - specifically from
"vtkNRRDReader.cxx"? That code is supposed to be called by the generic
reader, and it should give some more descriptive errors.

Isaiah


On Wed, 2010-01-13 at 07:12 +0100, Sarper Gürel wrote:

> Hello Isaiah
>
> Firstly, thanks for the sample nhdr file. I modified it accordingly
> and tried several combinations of properties. I still could not make
> the slicer read the data. After I press "Apply" on the "Add Volume",
> slicer always asks me to give the properties manually.
>
> On the error log i see:
> Type: Error
> Time: 01/13/10 07:02:36
> Description: ERROR: In
> ..\..\..\Slicer3\Libs\MRML\vtkMRMLVolumeArchetypeStorageNode.cxx, line
> 337
> vtkMRMLVolumeArchetypeStorageNode (163BAD98): reader 0th file name =
> C:/Tez/nhrdDeneme/Header.nhdr
>
>
>
> Type: Error
> Time: 01/13/10 07:02:36
> Description: ERROR: In
> ..\..\..\Slicer3\Libs\MRML\vtkMRMLVolumeArchetypeStorageNode.cxx, line
> 334
> vtkMRMLVolumeArchetypeStorageNode (163BAD98): ReadData: Cannot read
> file, fullName = C:/Tez/nhrdDeneme/Header.nhdr, node num file names =
> 0, reader num files = 1, reader archetype =
> C:/Tez/nhrdDeneme/Header.nhdr
>
>
> Is it possible to get a more detailed error description from slicer or
> another tool that reads nhdr?
>
> Thanks
>
> Sarper
>
>
> On Mon, Jan 11, 2010 at 7:00 PM, Isaiah Norton <[hidden email]> wrote:
> > Hi Sarper,
> >
> > Here is a sample nhdr to get you started:
> >
> > ---begin---
> > NRRD0005
> > content: epi-dti-asset
> > dimension: 4
> > sizes: 256 256 44 56
> > type: ushort
> > encoding: raw
> > endian: little
> > byte skip: -1
> > space: left-posterior-superior
> > space directions: (1.0, 0.0, 0.0) (0.0, 1.0, 0.0) (0.0, 0.0, 2.6) none
> > space units: "mm" "mm" "mm"
> > centers: cell cell cell none
> > kinds: space space space list
> > data file: 00%04d.IMA 1 1408 1 2
> > measurement frame: (1,0,0) (0,1,0) (0,0,-1)
> > modality:=DWMRI
> > ---end---
> >
> > Most of these should map directly. For "data file" yours should only
> > have one filename listed - the format above is file magic to select all
> > files meeting the criteria. Be sure to change the "content" and
> > "modality" tags to something more appropriate, or remove. HTH
> >
> > -Isaiah
> >
> > On Mon, 2010-01-11 at 08:46 -0500, Steve Pieper wrote:
> >> Hi Sarper -
> >>
> >> Probably the easiest is to create a slicer-compatible header that points
> >> to the data in your existing data file.  It looks like you have all the
> >> needed info.
> >>
> >> You could use a .nhdr file or a .mhd - see the info at the links below.
> >>
> >> Best,
> >> Steve
> >>
> >> http://teem.sourceforge.net/nrrd/format.html
> >>
> >> http://www.itk.org/Wiki/MetaIO
> >>
> >>
> >> On J/11/10 3:57 AM, Sarper Gürel wrote:
> >> > Hello people
> >> >
> >> > I am quite new to the slicer. I have a question about importing data
> >> > from other visualization software. I have a 3d dataset from "VGI Max"
> >> > software and I want to use it on Slicer 3.4. The following header
> >> > information is available for the dataset (It is actually a big single
> >> > file)
> >> >     ----------------------
> >> >     {volume1}
> >> >     [representation]
> >> >     size = 383 383 420
> >> >     resamplemode = not activated
> >> >     datatype = unsigned integer
> >> >     datarange = 0 -1
> >> >     bitsperelement = 8
> >> >     [file1]
> >> >     RegionOfInterestStart = 0 0 0
> >> >     RegionOfInterestEnd = 382 382 419
> >> >     SkipHeader = 22
> >> >     FileFormat = raw
> >> >     Size = 383 383 420
> >> >     Mirror = 0 0 1
> >> >     Name = C:/mydata.dat
> >> >     Datatype = unsigned integer
> >> >     BitsPerElement = 8
> >> >     ----------------------
> >> >
> >> > It tried several combination of properties in the Slicer module
> >> > "Volumes", but did not accomplished to see the data. Is Slicer capable
> >> > of reading this kind of file?
> >> >
> >> > Thanks in advance and greets from Switzerland.
> >> >
> >> > Sarper Gürel
> >> > _______________________________________________
> >> > slicer-users mailing list
> >> > [hidden email]
> >> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> >> > To unsubscribe: send email to [hidden email] with unsubscribe as the subject
> >> _______________________________________________
> >> slicer-users mailing list
> >> [hidden email]
> >> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> >> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
> >
> >
> >
> > The information in this e-mail is intended only for the person to whom it is
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> > contains patient information, please contact the Partners Compliance HelpLine at
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