[Insight-users] how to run the AtlasSegmentation example?

[Luis Ibanez]

Hi Elizabeth,


1) Did you obtained the appropriate data from the IBSR web site ?

         http://www.cma.mgh.harvard.edu/ibsr/intro.html



2) Did you actually put the data on a drive "I:" and in the exact
    same directory


                  I:/IBSR/20Normals_T1/   ??


    If not, you must edit the input_1.txt file and replace the first
    two lines with the real directories from your system where you
    put the images that you downloaded from IBSR.



3) The report


                   AtlasSegmentation.pdf


    is available as part of the InsightDocuments module,
    in the "Validation" subdirectory:

http://www.itk.org/cgi-bin/viewcvs.cgi/Validation/?root=InsightDocuments



    You can download the report from:

http://www.itk.org/cgi-bin/viewcvs.cgi/Validation/AtlasSegmentation/?root=InsightDocuments





Regards,



    Luis




----------------------------
Elizabeth R Jurrus wrote:

> Hello!
> 
> I'm trying to run the AtlasSegmentation code from 
> InsightApplications-1.8.0/IBSRValidation...  I get the following series 
> of errors:
> 
> ----------------
> [dione:~/vtk/InsightApplications-1.8.0/IBSRValidation/AtlasSegmentation] 
> % 
> ../../../InsightApplications-1.8.0_build/IBSRValidation/AtlasSegmentation/BrainStripValidationApp 
> Inputs/input_1.txt
> Running case:  atlas = 100_23 subject = 1_24
> Parsing input ...
> Error while reading in image for patient 100_23
> Error occurred during input parsing.
> Caught an ITK exception:
> 
> itk::ExceptionObject (0x83d2bc8)
> Location: "Unknown"
> File: /home/sci/liz/vtk/InsightToolkit-1.8.0/Code/IO/itkRawImageIO.txx
> Line: 114
> Description: itk::ERROR: RawImageIO(0x83d5cd8): Could not open file: 
> I:/IBSR/20Normals_T1/100_23/100_
> 23_1.img
> -------------------
> 
> I'm guessing the input file is out of date.  I've tried pointing the 
> input file to the right directory but there still appear to be some 
> missing pieces of information.  Any suggestions?
> 
> Also, where can I find the report called AtlasSegmentation.pdf 
> (referenced in the ReadMe.txt)?
> 
> Thanks!
> 
> - Liz
> _______________________________________________
> Insight-users mailing list
> Insight-users at itk.org
> http://www.itk.org/mailman/listinfo/insight-users
> 
>