[Insight-users] [ANNOUNCE] ITK 4.4.0 has been released!
Panagiotis Foteinos
panagiotis.foteinos at gmail.com
Fri Jul 12 12:33:41 EDT 2013
Thank you Vladimir for the image.
Yes, it works like a charm with your lower resolution image.
So, is it an ITK bug or a BigBrain bug? How should I proceed to read the
original image?
Best,
Panagiotis
On Thu, Jul 11, 2013 at 12:21 PM, Vladimir S. FONOV <
vladimir.fonov at gmail.com> wrote:
> 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<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<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@**gmail.com<panagiotis.foteinos at gmail.com>
>> >
>> <mailto:panagiotis.foteinos at __**gmail.com <http://gmail.com>
>> <mailto:panagiotis.foteinos@**gmail.com<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<bill.lorensen at gmail.com>
>> >
>> <mailto:bill.lorensen at gmail.__**com
>> <mailto:bill.lorensen at gmail.**com <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 <vladimir.fonov at gmail.com>>
>> <mailto:vladimir.fonov at gmail._**_com
>>
>> <mailto:vladimir.fonov at gmail.**com <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 <bill.lorensen at gmail.com>>
>> <mailto:bill.lorensen at gmail.__**com <mailto:bill.lorensen at gmail.*
>> *com <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 <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@**gmail.com<panagiotis.foteinos at gmail.com>
>> >
>> <mailto:panagiotis.foteinos at __**gmail.com<http://gmail.com>
>> <mailto:panagiotis.foteinos@**gmail.com<panagiotis.foteinos at gmail.com>
>> >>
>> <mailto:panagiotis.foteinos@
>> <mailto:panagiotis.foteinos@>_**___gmail.com <http://gmail.com>
>>
>>
>> <mailto:panagiotis.foteinos at __**gmail.com<http://gmail.com>
>> <mailto:panagiotis.foteinos@**gmail.com<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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