[Insight-users] [ANNOUNCE] ITK 4.4.0 has been released!
Vladimir S. FONOV
vladimir.fonov at gmail.com
Thu Jul 11 12:21:39 EDT 2013
Hello,
can you try running your ITK based program on this file:
http://www.bic.mni.mcgill.ca/~vfonov/temp/full16_100um_2009b_sym_lowres.mnc
it's the same volume downsampled to 1x1x1mm resolution.
On 13-07-10 05:48 PM, Panagiotis Foteinos wrote:
> Yes.
>
> This is indeed the file I tried to read. The very first file in the list
> of the "3D Volume" Tab.
>
> Best,
> Panagiotis
>
>
> On Wed, Jul 10, 2013 at 5:39 PM, Vladimir S. FONOV
> <vladimir.fonov at gmail.com <mailto:vladimir.fonov at gmail.com>> wrote:
>
> Hello,
>
>
> Assuming that file is not modified - I have it , it's 3Gb in size,
> md5sum 2aa33ed570da7ec0842f37bb5d0f38__da
> sha256sum
> 117d9d089e248f2ab0ef3d5571c82e__827668a8eba3ed8095fbbfaa7a0755__71c5
>
>
>
> On 13-07-10 05:34 PM, Bill Lorensen wrote:
>
> I have asked for the Big Brain Project for an account. I'll
> proceed once
> I get permission.
>
> The Big Brain Project is an exciting project and I hope ITK can
> access
> its data.
>
>
>
> On Wed, Jul 10, 2013 at 5:30 PM, Panagiotis Foteinos
> <panagiotis.foteinos at gmail.com
> <mailto:panagiotis.foteinos at gmail.com>
> <mailto:panagiotis.foteinos at __gmail.com
> <mailto:panagiotis.foteinos at gmail.com>>>
>
> wrote:
>
> Dear all,
> thank you for your advice.
>
> Vladimir: yes, this is the right file. However, my 64bit system
> machine has 96GB of memory, so RAM is not a problem.
> Actually, no
> RAM is being used, since it seems that the file is not even
> opened.
>
> Bill: Would you still like a pointer to the file?
>
> Best Regards,
> Panagiotis
>
>
> On Wed, Jul 10, 2013 at 5:09 PM, Bill Lorensen
> <bill.lorensen at gmail.com <mailto:bill.lorensen at gmail.com>
> <mailto:bill.lorensen at gmail.__com
> <mailto:bill.lorensen at gmail.com>>> wrote:
>
> Vladimir,
>
> I suspect that you are correct. This huge dataset will
> require
> special processing.
>
> Bill
>
>
>
> On Wed, Jul 10, 2013 at 5:06 PM, Vladimir S. FONOV
> <vladimir.fonov at gmail.com
> <mailto:vladimir.fonov at gmail.com>
> <mailto:vladimir.fonov at gmail.__com
> <mailto:vladimir.fonov at gmail.com>>> wrote:
>
> Hello,
>
> if it is the same file as the one from the bigbrain
> project,
> it has dimensions of 1970x2330x1890 , stored as
> unsigned
> short (2bytes per voxel), and required
> approximately 32Gb of
> ram to load it in memory - MINCImageIO will load
> the whole
> volume into memory as array of floats.
>
> Also, the volume is stored in YZX order , with Y
> fastest
> varying, because ITK only allows using XYZ order the
> MINCImageIO transposes the volume as part of
> loading it into
> memory.
>
> I have tried to load the whole volume into memory
> on a 64bit
> machine with 128Gb of ram using ITK-4.4 version and
> the test
> worked properly, although took a bit of time.
>
> Maybe the error appears when the machine does not
> have RAM?
>
>
> On 13-07-10 02:38 PM, Panagiotis Foteinos wrote:
>
> It is the first mnc file I have ever worked on.
>
> Let me see how other software behaves, and I
> will report
> back.
>
> Thank you,
> Panagiotis
>
>
> On Wed, Jul 10, 2013 at 2:35 PM, Bill Lorensen
> <bill.lorensen at gmail.com
> <mailto:bill.lorensen at gmail.com>
> <mailto:bill.lorensen at gmail.__com <mailto:bill.lorensen at gmail.com>>
> <mailto:bill.lorensen at gmail.
> <mailto:bill.lorensen at gmail.>____com
>
> <mailto:bill.lorensen at gmail.__com
> <mailto:bill.lorensen at gmail.com>>>> wrote:
>
> Have you ever read this file with other
> software?
> Have you tried
> other mnc files?
>
>
> On Wed, Jul 10, 2013 at 2:25 PM,
> Panagiotis Foteinos
> <panagiotis.foteinos at gmail.com
> <mailto:panagiotis.foteinos at gmail.com>
> <mailto:panagiotis.foteinos at __gmail.com
> <mailto:panagiotis.foteinos at gmail.com>>
> <mailto:panagiotis.foteinos@
> <mailto:panagiotis.foteinos@>____gmail.com <http://gmail.com>
>
> <mailto:panagiotis.foteinos at __gmail.com
> <mailto:panagiotis.foteinos at gmail.com>>>> wrote:
>
> I have given all the permissions to
> the file in
> question.
>
> The error I am getting is:
>
> *********************
>
>
> /home/pfoteino/local/bin/itk-____4.4.0-bin/release/Modules/____ThirdParty/MINC/ITKMINC2_____ExternalProject/libsrc2/____volume.c:142
>
> (from MINC2): Unable to open file
>
>
> '/home/pfoteino/ITK_Images/____BigBrain/full16_100um_2009b_____sym.mnc'
>
> ExceptionObject caught!
>
> itk::ExceptionObject (0x28ab790)
> Location: "unknown"
> File:
>
>
> /home/pfoteino/local/src/ITK-____4.4.0/Modules/IO/ImageBase/____src/itkImageIOBase.cxx
>
> Line: 366
> Description: itk::ERROR:
> MINCImageIO(0x28aecf0): Unknown
> component type: 0
>
>
>
> --
> Best regards,
>
> Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com <http://gmail.com>
>
>
--
Best regards,
Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
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