<div dir="ltr">Yes.<div><br></div><div style>This is indeed the file I tried to read. The very first file in the list of the "3D Volume" Tab.</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 Wed, Jul 10, 2013 at 5:39 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>
Assuming that file is not modified - I have it , it's 3Gb in size, md5sum 2aa33ed570da7ec0842f37bb5d0f38<u></u>da<br>
sha256sum 117d9d089e248f2ab0ef3d5571c82e<u></u>827668a8eba3ed8095fbbfaa7a0755<u></u>71c5<div class="im"><br>
<br>
<br>
On 13-07-10 05:34 PM, Bill Lorensen wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
I have asked for the Big Brain Project for an account. I'll proceed once<br>
I get permission.<br>
<br>
The Big Brain Project is an exciting project and I hope ITK can access<br>
its data.<br>
<br>
<br>
<br>
On Wed, Jul 10, 2013 at 5:30 PM, Panagiotis Foteinos<br></div>
<<a href="mailto:panagiotis.foteinos@gmail.com" target="_blank">panagiotis.foteinos@gmail.com</a> <mailto:<a href="mailto:panagiotis.foteinos@gmail.com" target="_blank">panagiotis.foteinos@<u></u>gmail.com</a>>><div class="im">
<br>
wrote:<br>
<br>
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. Actually, no<br>
RAM is being used, since it seems that the file is not even 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></div><div class="im">
<<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>>> wrote:<br>
<br>
Vladimir,<br>
<br>
I suspect that you are correct. This huge dataset will require<br>
special processing.<br>
<br>
Bill<br>
<br>
<br>
<br>
On Wed, Jul 10, 2013 at 5:06 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>
if it is the same file as the one from the bigbrain project,<br>
it has dimensions of 1970x2330x1890 , stored as unsigned<br>
short (2bytes per voxel), and required approximately 32Gb of<br>
ram to load it in memory - MINCImageIO will load the whole<br>
volume into memory as array of floats.<br>
<br>
Also, the volume is stored in YZX order , with Y fastest<br>
varying, because ITK only allows using XYZ order the<br>
MINCImageIO transposes the volume as part of loading it into<br>
memory.<br>
<br>
I have tried to load the whole volume into memory on a 64bit<br>
machine with 128Gb of ram using ITK-4.4 version and the test<br>
worked properly, although took a bit of time.<br>
<br>
Maybe the error appears when the machine does not 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 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> <mailto:<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.<u></u>com</a>><br></div>
<mailto:<a href="mailto:bill.lorensen@gmail." target="_blank">bill.lorensen@gmail.</a>__<u></u>com<div class="im"><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 software?<br>
Have you tried<br>
other mnc files?<br>
<br>
<br>
On Wed, Jul 10, 2013 at 2:25 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>
<mailto:<a href="mailto:panagiotis.foteinos@" target="_blank">panagiotis.foteinos@</a>__<a href="http://gmail.com" target="_blank"><u></u>gmail.com</a><div class="im"><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 the file in<br>
question.<br>
<br>
The error I am getting is:<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>
(from MINC2): Unable to open file<br>
<br></div>
'/home/pfoteino/ITK_Images/__<u></u>BigBrain/full16_100um_2009b___<u></u>sym.mnc'<div class="im"><br>
ExceptionObject caught!<br>
<br>
itk::ExceptionObject (0x28ab790)<br>
Location: "unknown"<br>
File:<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>
Line: 366<br>
Description: itk::ERROR:<br>
MINCImageIO(0x28aecf0): Unknown<br>
component type: 0<br>
</div></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>