[Insight-users] [ANNOUNCE] ITK 4.4.0 has been released!
Bill Lorensen
bill.lorensen at gmail.com
Fri Jul 12 12:36:32 EDT 2013
These big brain images are quite new. Maybe try the nifti format.
On Fri, Jul 12, 2013 at 12:33 PM, Panagiotis Foteinos <
panagiotis.foteinos at gmail.com> wrote:
> 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
>>
>
>
--
Unpaid intern in BillsBasement at noware dot com
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