<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>Shareable test data greatly helps determine the cause and fix these types of issues.</div><div><br></div><div>Got data?</div><div><br></div><div>Brad<br><br></div><div><br>On Nov 23, 2014, at 5:40 PM, Gib Bogle <<a href="mailto:g.bogle@auckland.ac.nz">g.bogle@auckland.ac.nz</a>> wrote:<br><br></div><blockquote type="cite"><div>
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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">This is reminiscent of the previous problem with big TIFF images, now fixed.<br>
<br>
Gib<br>
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<div style="direction: ltr;" id="divRpF783081"><font color="#000000" face="Tahoma" size="2"><b>From:</b> Insight-users [<a href="mailto:insight-users-bounces@itk.org">insight-users-bounces@itk.org</a>] on behalf of Fotis Drakopoulos [<a href="mailto:fdrakopo@gmail.com">fdrakopo@gmail.com</a>]<br>
<b>Sent:</b> Monday, 24 November 2014 10:51 a.m.<br>
<b>To:</b> <a href="mailto:insight-users@itk.org">insight-users@itk.org</a>; <a href="mailto:insight-developers@itk.org">insight-developers@itk.org</a><br>
<b>Subject:</b> [ITK-users] Problem reading a big nifti volume.<br>
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<div dir="ltr">Hi all,
<div><br>
</div>
<div>For the last couple of days I have been trying reading (unsuccessfully) a big nifti volume labeled image from my disk.</div>
<div><br>
</div>
<div>The pixel type is unsigned char and the rest specs of the image are:</div>
<div>Size : [1001, 1001, 8345] (in voxels)<br>
</div>
<div>
<div>Spacing : [0.012, 0.012, 0.012] (in mm)</div>
<div>Origin : [0, 0, 0]</div>
<div>Direction : </div>
<div>1 0 0</div>
<div>0 1 0</div>
<div>0 0 1</div>
</div>
<div><br>
</div>
<div>First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an idea how it looks like. Indeed the object in the volume looks as it was expected. So far no problems. The specs of the image on Slicer are the same as above (except the direction which
has flipped signs for the first two diagonal entries, as we know ).</div>
<div><br>
</div>
<div>Then I tried to load the image in the memory using the itk::ImageFileReader from ITK4.6.0 (64 bit-linux) version. After loading the image I noticed that there are pixels with zero values instead of non-zero by comparing the same indexes with the loaded
image on Slicer.</div>
<div><br>
</div>
<div>Then I decided to write the loaded image on the disk using the itk::ImageFileWriter. </div>
<div><br>
</div>
<div>After opening the (written from ITK) image on Slicer I checked the specks and were the same with the original image as above. However I noticed that a big portion of the image is completely empty (black)!</div>
<div><br>
</div>
<div>My workstation has enough memory to load the image (<span style="font-family:arial,sans-serif; font-size:13.333333969116211px">768 GB 1600MHz DDR3L</span>) and is using <span style="font-family:arial,sans-serif; font-size:13.333333969116211px">Red Hat
Enterprise Linux Server 6.5. </span></div>
<div><span style="font-family:arial,sans-serif; font-size:13.333333969116211px">The size of the original nifti volume is :</span></div>
<div>
<ul>
<li><span style="font-family:arial,sans-serif">25.7 MB (.nii.gz)</span><br>
</li><li><font face="arial, sans-serif">8.36 GB (.nii)</font><br>
</li></ul>
</div>
<div>Has anybody experienced similar difficulties trying to load so big volume data?</div>
<div><br>
</div>
<div>Best,</div>
<div>Fotis Drakopoulos</div>
<div>CRTC</div>
<div> </div>
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