<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">So if you wrote and read with ITK ( via Slicer ), how do you know that the file is correct as you expect?<div><br></div><div>I see the file has a ".nii.gz" extension, meaning that it's compressed. Does the same issue occur when it's not compressed?</div><div><br></div><div>Brad<br><div><br></div><div><br><div><div>On Dec 2, 2014, at 10:49 AM, Fotis Drakopoulos <<a href="mailto:fdrakopo@gmail.com">fdrakopo@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><div dir="ltr"><div>Hi,</div><div><br></div><div>I created and wrote the image on the disk using ITK 4.6.0. </div>I visualized the image using Slicer 4.4.0.<div><br></div><div>The properties are:</div><div><div style="font-family:arial,sans-serif;font-size:13.333333969116211px">Size : [1001, 1001, 8345] <br></div><div style="font-family:arial,sans-serif;font-size:13.333333969116211px">Spacing : [1,1,1]</div><div><div><font face="arial, sans-serif">Origin : [0, 0, 0]</font></div><div><font face="arial, sans-serif">Direction : </font></div><div><font face="arial, sans-serif">1 0 0</font></div><div><font face="arial, sans-serif">0 1 0</font></div><div><font face="arial, sans-serif">0 0 1</font></div></div><div><br></div><div>Fotis</div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Dec 2, 2014 at 10:27 AM, Bradley Lowekamp <span dir="ltr"><<a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hello,<div><br></div><div>What software did you use to create and validate that this image is correct?</div><div><br></div><div>Thanks,</div><div>Brad</div><div><br><div><div><div class="h5"><div>On Dec 1, 2014, at 11:56 AM, Fotis Drakopoulos <<a href="mailto:fdrakopo@gmail.com" target="_blank">fdrakopo@gmail.com</a>> wrote:</div><br></div></div><blockquote type="cite"><div><div class="h5"><div dir="ltr">Hi all,<div><br></div><div>I added a big test image<span style="font-size:13.333333969116211px;font-family:arial,sans-serif"> to ITK/Public/ITK/Modules/IO/</span><span style="font-size:13.333333969116211px;font-family:arial,sans-serif">NIFTI/test/Input. The image cannot loaded correctly when I use the </span><span style="font-family:arial,sans-serif;font-size:13.333333969116211px">itk::ImageFileReader.</span></div><div>The test image contains non-zero values only at indexes (350,350,i) where i=0 to 8300.</div><div>The pixelType is short.</div><div> </div><div>Thanks</div><div>Fotis </div></div></div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="h5">On Wed, Nov 26, 2014 at 8:41 PM, Matt McCormick <span dir="ltr"><<a href="mailto:matt.mccormick@kitware.com" target="_blank">matt.mccormick@kitware.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">Thanks! Added.<br>
<div><br>
On Wed, Nov 26, 2014 at 9:21 AM, Fotis Drakopoulos <<a href="mailto:fdrakopo@gmail.com" target="_blank">fdrakopo@gmail.com</a>> wrote:<br>
> Hi,<br>
> I signed up for the ITK community on midas.<br>
><br>
> Thanks,<br>
> Fotis Drakopoulos<br>
><br>
> On Tue, Nov 25, 2014 at 10:44 PM, Matt McCormick<br>
> <<a href="mailto:matt.mccormick@kitware.com" target="_blank">matt.mccormick@kitware.com</a>> wrote:<br>
>><br>
>> Hi Fotis,<br>
>><br>
>> Thanks for helping to improve large nifti file support.<br>
>><br>
>> The file can be uploaded on <a href="http://midas3.kitware.com/" target="_blank">midas3.kitware.com</a>. Sign up for the ITK<br>
>> community [1], let the list know the name of your account, and myself<br>
>> or one of the other administrators will add upload priviledges to the<br>
>> account.<br>
>><br>
>> The file could then be added to<br>
>> ITK/Public/ITK/Modules/IO/NIFTI/test/Input.<br>
>><br>
>> Thanks,<br>
>> Matt<br>
>><br>
>> [1] <a href="http://midas3.kitware.com/midas/community/12" target="_blank">http://midas3.kitware.com/midas/community/12</a><br>
>><br>
>> On Tue, Nov 25, 2014 at 3:14 PM, Fotis Drakopoulos <<a href="mailto:fdrakopo@gmail.com" target="_blank">fdrakopo@gmail.com</a>><br>
>> wrote:<br>
>> > Hi all,<br>
>> ><br>
>> > I created a test nifti image that reproduces the problem I mentioned<br>
>> > before.<br>
>> > How can I share this image with the ITK community?<br>
>> ><br>
>> > Best,<br>
>> > Fotis Drakopoulos<br>
>> ><br>
>> ><br>
>> > On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp<br>
>> > <<a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a>><br>
>> > wrote:<br>
>> >><br>
>> >> Shareable test data greatly helps determine the cause and fix these<br>
>> >> types<br>
>> >> of issues.<br>
>> >><br>
>> >> Got data?<br>
>> >><br>
>> >> Brad<br>
>> >> On Nov 23, 2014, at 5:40 PM, Gib Bogle <<a href="mailto:g.bogle@auckland.ac.nz" target="_blank">g.bogle@auckland.ac.nz</a>> wrote:<br>
>> >><br>
>> >> This is reminiscent of the previous problem with big TIFF images, now<br>
>> >> fixed.<br>
>> >><br>
>> >> Gib<br>
>> >> ________________________________<br>
>> >> From: Insight-users [<a href="mailto:insight-users-bounces@itk.org" target="_blank">insight-users-bounces@itk.org</a>] on behalf of Fotis<br>
>> >> Drakopoulos [<a href="mailto:fdrakopo@gmail.com" target="_blank">fdrakopo@gmail.com</a>]<br>
>> >> Sent: Monday, 24 November 2014 10:51 a.m.<br>
>> >> To: <a href="mailto:insight-users@itk.org" target="_blank">insight-users@itk.org</a>; <a href="mailto:insight-developers@itk.org" target="_blank">insight-developers@itk.org</a><br>
>> >> Subject: [ITK-users] Problem reading a big nifti volume.<br>
>> >><br>
>> >> Hi all,<br>
>> >><br>
>> >> For the last couple of days I have been trying reading (unsuccessfully)<br>
>> >> a<br>
>> >> big nifti volume labeled image from my disk.<br>
>> >><br>
>> >> The pixel type is unsigned char and the rest specs of the image are:<br>
>> >> Size : [1001, 1001, 8345] (in voxels)<br>
>> >> Spacing : [0.012, 0.012, 0.012] (in mm)<br>
>> >> Origin : [0, 0, 0]<br>
>> >> Direction :<br>
>> >> 1 0 0<br>
>> >> 0 1 0<br>
>> >> 0 0 1<br>
>> >><br>
>> >> First I loaded the volume on Slicer-4.4.0 (64 bit-linux) to get an idea<br>
>> >> how it looks like. Indeed the object in the volume looks as it was<br>
>> >> expected.<br>
>> >> So far no problems. The specs of the image on Slicer are the same as<br>
>> >> above<br>
>> >> (except the direction which has flipped signs for the first two<br>
>> >> diagonal<br>
>> >> entries, as we know ).<br>
>> >><br>
>> >> Then I tried to load the image in the memory using the<br>
>> >> itk::ImageFileReader from ITK4.6.0 (64 bit-linux) version. After<br>
>> >> loading<br>
>> >> the image I noticed that there are pixels with zero values instead of<br>
>> >> non-zero by comparing the same indexes with the loaded image on Slicer.<br>
>> >><br>
>> >> Then I decided to write the loaded image on the disk using the<br>
>> >> itk::ImageFileWriter.<br>
>> >><br>
>> >> After opening the (written from ITK) image on Slicer I checked the<br>
>> >> specks<br>
>> >> and were the same with the original image as above. However I noticed<br>
>> >> that a<br>
>> >> big portion of the image is completely empty (black)!<br>
>> >><br>
>> >> My workstation has enough memory to load the image (768 GB 1600MHz<br>
>> >> DDR3L)<br>
>> >> and is using Red Hat Enterprise Linux Server 6.5.<br>
>> >> The size of the original nifti volume is :<br>
>> >><br>
>> >> 25.7 MB (.nii.gz)<br>
>> >> 8.36 GB (.nii)<br>
>> >><br>
>> >> Has anybody experienced similar difficulties trying to load so big<br>
>> >> volume<br>
>> >> data?<br>
>> >><br>
>> >> Best,<br>
>> >> Fotis Drakopoulos<br>
>> >> CRTC<br>
>> >><br>
>> >> _____________________________________<br>
>> >> Powered by <a href="http://www.kitware.com/" target="_blank">www.kitware.com</a><br>
>> >><br>
>> >> Visit other Kitware open-source projects at<br>
>> >> <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
>> >><br>
>> >> Kitware offers ITK Training Courses, for more information visit:<br>
>> >> <a href="http://www.kitware.com/products/protraining.php" target="_blank">http://www.kitware.com/products/protraining.php</a><br>
>> >><br>
>> >> Please keep messages on-topic and check the ITK FAQ at:<br>
>> >> <a href="http://www.itk.org/Wiki/ITK_FAQ" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br>
>> >><br>
>> >> Follow this link to subscribe/unsubscribe:<br>
>> >> <a href="http://public.kitware.com/mailman/listinfo/insight-users" target="_blank">http://public.kitware.com/mailman/listinfo/insight-users</a><br>
>> >><br>
>> >><br>
>> >> ________________________________<br>
>> >><br>
>> >> Spam<br>
>> >> Not spam<br>
>> >> Forget previous vote<br>
>> ><br>
>> ><br>
>> ><br>
>> > _______________________________________________<br>
>> > Powered by <a href="http://www.kitware.com/" target="_blank">www.kitware.com</a><br>
>> ><br>
>> > Visit other Kitware open-source projects at<br>
>> > <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
>> ><br>
>> > Kitware offers ITK Training Courses, for more information visit:<br>
>> > <a href="http://kitware.com/products/protraining.php" target="_blank">http://kitware.com/products/protraining.php</a><br>
>> ><br>
>> > Please keep messages on-topic and check the ITK FAQ at:<br>
>> > <a href="http://www.itk.org/Wiki/ITK_FAQ" target="_blank">http://www.itk.org/Wiki/ITK_FAQ</a><br>
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>><br>
>><br>
>> --<br>
>><br>
><br>
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