<div dir="ltr">Thank you Vladimir for the image.<div><br></div><div style>Yes, it works like a charm with your lower resolution image. </div><div style><br></div><div style>So, is it an ITK bug or a BigBrain bug? How should I proceed to read the original image?</div>
<div style><br></div><div style>Best,</div><div style>Panagiotis</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Jul 11, 2013 at 12:21 PM, Vladimir S. FONOV <span dir="ltr"><<a href="mailto:vladimir.fonov@gmail.com" target="_blank">vladimir.fonov@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hello,<br>
<br>
<br>
can you try running your ITK based program on this file: <a href="http://www.bic.mni.mcgill.ca/~vfonov/temp/full16_100um_2009b_sym_lowres.mnc" target="_blank">http://www.bic.mni.mcgill.ca/~<u></u>vfonov/temp/full16_100um_<u></u>2009b_sym_lowres.mnc</a><br>
<br>
it's the same volume downsampled to 1x1x1mm resolution.<div class="im"><br>
<br>
On 13-07-10 05:48 PM, Panagiotis Foteinos wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
Yes.<br>
<br>
This is indeed the file I tried to read. The very first file in the list<br>
of the "3D Volume" Tab.<br>
<br>
Best,<br>
Panagiotis<br>
<br>
<br>
On Wed, Jul 10, 2013 at 5:39 PM, Vladimir S. FONOV<br></div><div class="im">
<<a href="mailto:vladimir.fonov@gmail.com" target="_blank">vladimir.fonov@gmail.com</a> <mailto:<a href="mailto:vladimir.fonov@gmail.com" target="_blank">vladimir.fonov@gmail.<u></u>com</a>>> wrote:<br>
<br>
Hello,<br>
<br>
<br>
Assuming that file is not modified - I have it , it's 3Gb in size,<br></div>
md5sum 2aa33ed570da7ec0842f37bb5d0f38<u></u>__da<br>
sha256sum<br>
117d9d089e248f2ab0ef3d5571c82e<u></u>__<u></u>827668a8eba3ed8095fbbfaa7a0755<u></u>__71c5<div class="im"><br>
<br>
<br>
<br>
On 13-07-10 05:34 PM, Bill Lorensen wrote:<br>
<br>
I have asked for the Big Brain Project for an account. I'll<br>
proceed once<br>
I get permission.<br>
<br>
The Big Brain Project is an exciting project and I hope ITK can<br>
access<br>
its data.<br>
<br>
<br>
<br>
On Wed, Jul 10, 2013 at 5:30 PM, Panagiotis Foteinos<br>
<<a href="mailto:panagiotis.foteinos@gmail.com" target="_blank">panagiotis.foteinos@gmail.com</a><br>
<mailto:<a href="mailto:panagiotis.foteinos@gmail.com" target="_blank">panagiotis.foteinos@<u></u>gmail.com</a>><br></div><div class="im">
<mailto:<a href="mailto:panagiotis.foteinos@" target="_blank">panagiotis.foteinos@</a>__<a href="http://gmail.com" target="_blank"><u></u>gmail.com</a><br>
<mailto:<a href="mailto:panagiotis.foteinos@gmail.com" target="_blank">panagiotis.foteinos@<u></u>gmail.com</a>>>><br>
<br>
wrote:<br>
<br></div><div class="im">
Dear all,<br>
thank you for your advice.<br>
<br>
Vladimir: yes, this is the right file. However, my 64bit system<br>
machine has 96GB of memory, so RAM is not a problem.<br>
Actually, no<br>
RAM is being used, since it seems that the file is not even<br>
opened.<br>
<br>
Bill: Would you still like a pointer to the file?<br>
<br>
Best Regards,<br>
Panagiotis<br>
<br>
<br>
On Wed, Jul 10, 2013 at 5:09 PM, Bill Lorensen<br>
<<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a> <mailto:<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.<u></u>com</a>><br></div><div class="im">
<mailto:<a href="mailto:bill.lorensen@gmail." target="_blank">bill.lorensen@gmail.</a>__<u></u>com<br>
<mailto:<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.<u></u>com</a>>>> wrote:<br>
<br></div><div class="im">
Vladimir,<br>
<br>
I suspect that you are correct. This huge dataset will<br>
require<br>
special processing.<br>
<br>
Bill<br>
<br>
<br>
<br>
On Wed, Jul 10, 2013 at 5:06 PM, Vladimir S. FONOV<br>
<<a href="mailto:vladimir.fonov@gmail.com" target="_blank">vladimir.fonov@gmail.com</a><br>
<mailto:<a href="mailto:vladimir.fonov@gmail.com" target="_blank">vladimir.fonov@gmail.<u></u>com</a>><br></div>
<mailto:<a href="mailto:vladimir.fonov@gmail." target="_blank">vladimir.fonov@gmail.</a>_<u></u>_com<div><div class="h5"><br>
<mailto:<a href="mailto:vladimir.fonov@gmail.com" target="_blank">vladimir.fonov@gmail.<u></u>com</a>>>> wrote:<br>
<br>
Hello,<br>
<br>
if it is the same file as the one from the bigbrain<br>
project,<br>
it has dimensions of 1970x2330x1890 , stored as<br>
unsigned<br>
short (2bytes per voxel), and required<br>
approximately 32Gb of<br>
ram to load it in memory - MINCImageIO will load<br>
the whole<br>
volume into memory as array of floats.<br>
<br>
Also, the volume is stored in YZX order , with Y<br>
fastest<br>
varying, because ITK only allows using XYZ order the<br>
MINCImageIO transposes the volume as part of<br>
loading it into<br>
memory.<br>
<br>
I have tried to load the whole volume into memory<br>
on a 64bit<br>
machine with 128Gb of ram using ITK-4.4 version and<br>
the test<br>
worked properly, although took a bit of time.<br>
<br>
Maybe the error appears when the machine does not<br>
have RAM?<br>
<br>
<br>
On 13-07-10 02:38 PM, Panagiotis Foteinos wrote:<br>
<br>
It is the first mnc file I have ever worked on.<br>
<br>
Let me see how other software behaves, and I<br>
will report<br>
back.<br>
<br>
Thank you,<br>
Panagiotis<br>
<br>
<br>
On Wed, Jul 10, 2013 at 2:35 PM, Bill Lorensen<br>
<<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a><br>
<mailto:<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.<u></u>com</a>><br>
<mailto:<a href="mailto:bill.lorensen@gmail." target="_blank">bill.lorensen@gmail.</a>__<u></u>com <mailto:<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.<u></u>com</a>>><br>
</div></div>
<mailto:<a href="mailto:bill.lorensen@gmail" target="_blank">bill.lorensen@gmail</a>.<br>
<mailto:<a href="mailto:bill.lorensen@gmail" target="_blank">bill.lorensen@gmail</a>.>_<u></u>___com<div class="im"><br>
<br>
<mailto:<a href="mailto:bill.lorensen@gmail." target="_blank">bill.lorensen@gmail.</a>__<u></u>com<br>
<mailto:<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.<u></u>com</a>>>>> wrote:<br>
<br>
Have you ever read this file with other<br>
software?<br>
Have you tried<br>
other mnc files?<br>
<br>
<br>
On Wed, Jul 10, 2013 at 2:25 PM,<br>
Panagiotis Foteinos<br>
<<a href="mailto:panagiotis.foteinos@gmail.com" target="_blank">panagiotis.foteinos@gmail.com</a><br>
<mailto:<a href="mailto:panagiotis.foteinos@gmail.com" target="_blank">panagiotis.foteinos@<u></u>gmail.com</a>><br>
<mailto:<a href="mailto:panagiotis.foteinos@" target="_blank">panagiotis.foteinos@</a>__<a href="http://gmail.com" target="_blank"><u></u>gmail.com</a><br>
<mailto:<a href="mailto:panagiotis.foteinos@gmail.com" target="_blank">panagiotis.foteinos@<u></u>gmail.com</a>>><br></div>
<mailto:<a href="mailto:panagiotis.foteinos@" target="_blank">panagiotis.foteinos@</a><br>
<mailto:<a href="mailto:panagiotis.foteinos@" target="_blank">panagiotis.foteinos@</a>>_<u></u>___<a href="http://gmail.com" target="_blank">gmail.com</a> <<a href="http://gmail.com" target="_blank">http://gmail.com</a>><div class="im">
<br>
<br>
<mailto:<a href="mailto:panagiotis.foteinos@" target="_blank">panagiotis.foteinos@</a>__<a href="http://gmail.com" target="_blank"><u></u>gmail.com</a><br>
<mailto:<a href="mailto:panagiotis.foteinos@gmail.com" target="_blank">panagiotis.foteinos@<u></u>gmail.com</a>>>>> wrote:<br>
<br>
I have given all the permissions to<br>
the file in<br>
question.<br>
<br>
The error I am getting is:<br>
<br>
*********************<br>
<br>
<br></div>
/home/pfoteino/local/bin/itk-_<u></u>___4.4.0-bin/release/Modules/_<u></u>___ThirdParty/MINC/ITKMINC2___<u></u>__ExternalProject/libsrc2/____<u></u>volume.c:142<div class="im"><br>
<br>
(from MINC2): Unable to open file<br>
<br>
<br></div>
'/home/pfoteino/ITK_Images/___<u></u>_BigBrain/full16_100um_2009b__<u></u>___sym.mnc'<div class="im"><br>
<br>
ExceptionObject caught!<br>
<br>
itk::ExceptionObject (0x28ab790)<br>
Location: "unknown"<br>
File:<br>
<br>
<br></div>
/home/pfoteino/local/src/ITK-_<u></u>___4.4.0/Modules/IO/ImageBase/<u></u>____src/itkImageIOBase.cxx<div class="im"><br>
<br>
Line: 366<br>
Description: itk::ERROR:<br>
MINCImageIO(0x28aecf0): Unknown<br>
component type: 0<br>
<br>
<br>
<br>
--<br>
Best regards,<br>
<br></div>
Vladimir S. FONOV ~ vladimir.fonov <at> <a href="http://gmail.com" target="_blank">gmail.com</a> <<a href="http://gmail.com" target="_blank">http://gmail.com</a>><br>
<br>
<br>
</blockquote><div class="HOEnZb"><div class="h5">
<br>
<br>
-- <br>
Best regards,<br>
<br>
Vladimir S. FONOV ~ vladimir.fonov <at> <a href="http://gmail.com" target="_blank">gmail.com</a><br>
</div></div></blockquote></div><br></div>