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<div class="moz-cite-prefix">Hi,<br>
Have you correctly specified the pixel type? I had similar problem
and mine was due to pixels specifications.<br>
Hope it helps.<br>
<br>
<pre class="moz-signature" cols="72">Jerome Plumat
-------
School of Medical Sciences
University of Auckland
If I am not for myself, who will be for me? And if I am only for myself, then what an I? And if not now when? – Hillel HaZaken</pre>
On 24/11/14 10:51, Fotis Drakopoulos wrote:<br>
</div>
<blockquote
cite="mid:CAG6AjROMWzAEWptqC3XmamwqDmwPc88d2YDup84tkDg20ZJdxw@mail.gmail.com"
type="cite">
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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>
</div>
<br>
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</blockquote>
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