<div dir="ltr"><br><div class="gmail_extra"><br><div class="gmail_quote">Can someone share the link to the software guide repository? I would be very interested to take a look.</div><div class="gmail_quote"><br></div><div class="gmail_quote"><br></div><div class="gmail_quote"><br></div><div class="gmail_quote">On Tue, Nov 25, 2014 at 3:14 PM, <span dir="ltr"><<a href="mailto:community-request@itk.org" target="_blank">community-request@itk.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Community mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Re: [ITK-dev] ITK Software Guide Printing (Johnson, Hans J)<br>
2. Re: [ITK-dev] [ITK-users] Problem reading a big nifti volume.<br>
(Fotis Drakopoulos)<br>
3. Re: [ITK-users] Problem reading a big nifti volume.<br>
(Fotis Drakopoulos)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 25 Nov 2014 14:55:49 +0000<br>
From: "Johnson, Hans J" <<a href="mailto:hans-johnson@uiowa.edu">hans-johnson@uiowa.edu</a>><br>
To: Matt McCormick <<a href="mailto:matt.mccormick@kitware.com">matt.mccormick@kitware.com</a>><br>
Cc: ITK <<a href="mailto:insight-developers@itk.org">insight-developers@itk.org</a>>, Christopher Mullins<br>
<<a href="mailto:christopher.mullins@kitware.com">christopher.mullins@kitware.com</a>><br>
Subject: Re: [ITK] [ITK-dev] ITK Software Guide Printing<br>
Message-ID: <<a href="mailto:3549BA92-5B59-4300-A0B4-7CD41E696A2D@uiowa.edu">3549BA92-5B59-4300-A0B4-7CD41E696A2D@uiowa.edu</a>><br>
Content-Type: text/plain; charset="us-ascii"<br>
<br>
I build the software guide last night. If we are targeting a 4.7 synchronization, then we need to update to a more recent codebase.<br>
<br>
A new gerri-patch pushed UpdateITKToNear4.7.<br>
<br>
Hans<br>
<br>
On Nov 25, 2014, at 7:06 AM, Matt McCormick <<a href="mailto:matt.mccormick@kitware.com">matt.mccormick@kitware.com</a><mailto:<a href="mailto:matt.mccormick@kitware.com">matt.mccormick@kitware.com</a>>> wrote:<br>
<br>
I think we could use some help with any warnings, especially for Book<br>
1. Thank you!<br>
<br>
On Mon, Nov 24, 2014 at 4:32 PM, <<a href="mailto:michkapopoff@gmail.com">michkapopoff@gmail.com</a><mailto:<a href="mailto:michkapopoff@gmail.com">michkapopoff@gmail.com</a>>> wrote:<br>
Cool :)<br>
<br>
I see that we have still some errors on the software guide dashboard:<br>
warning: Line length too long for LaTeX printing<br>
<br>
Will Christopher Mullins have time to work on this before printing, or do<br>
you need some help<br>
to fix the remaining warnings ?<br>
<br>
Michka<br>
<br>
On 24 Nov 2014, at 22:26, Matt McCormick <<a href="mailto:matt.mccormick@kitware.com">matt.mccormick@kitware.com</a><mailto:<a href="mailto:matt.mccormick@kitware.com">matt.mccormick@kitware.com</a>>> wrote:<br>
<br>
Hi,<br>
<br>
We are scheduled to have the ITK Software Guide sent to the printers<br>
next week so the physical books will be available for the 4.7 release.<br>
Please have any changes reviewed in Gerrit over the next week.<br>
<br>
Thanks,<br>
Matt<br>
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<br>
Message: 2<br>
Date: Tue, 25 Nov 2014 15:14:38 -0500<br>
From: Fotis Drakopoulos <<a href="mailto:fdrakopo@gmail.com">fdrakopo@gmail.com</a>><br>
To: Bradley Lowekamp <<a href="mailto:blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a>><br>
Cc: "<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>" <<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>>,<br>
"<a href="mailto:insight-developers@itk.org">insight-developers@itk.org</a>" <<a href="mailto:insight-developers@itk.org">insight-developers@itk.org</a>><br>
Subject: Re: [ITK] [ITK-dev] [ITK-users] Problem reading a big nifti<br>
volume.<br>
Message-ID:<br>
<<a href="mailto:CAG6AjRNaVdcxH1ScfVx-k3dXx8i2obffjvtLRvvLqPG1xnCSaA@mail.gmail.com">CAG6AjRNaVdcxH1ScfVx-k3dXx8i2obffjvtLRvvLqPG1xnCSaA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi all,<br>
<br>
I created a test nifti image that reproduces the problem I mentioned 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 <<a href="mailto:blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a>><br>
wrote:<br>
<br>
> Shareable test data greatly helps determine the cause and fix these 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">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">insight-users-bounces@itk.org</a>] on behalf of Fotis<br>
> Drakopoulos [<a href="mailto:fdrakopo@gmail.com">fdrakopo@gmail.com</a>]<br>
> *Sent:* Monday, 24 November 2014 10:51 a.m.<br>
> *To:* <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>
> *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) 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. So far no problems. The specs of the image on Slicer are the same<br>
> as above (except the direction which has flipped signs for the first two<br>
> diagonal 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 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 specks<br>
> and were the same with the original image as above. However I noticed that<br>
> a big portion of the image is completely empty (black)!<br>
><br>
> My workstation has enough memory to load the image (768 GB 1600MHz 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 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>
> <<a href="https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=s" target="_blank">https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=s</a>><br>
> Not spam<br>
> <<a href="https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=n" target="_blank">https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=n</a>><br>
> Forget previous vote<br>
> <<a href="https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=f" target="_blank">https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=f</a>><br>
><br>
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_______________________________________________<br>
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<br>
Visit other Kitware open-source projects at<br>
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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>
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------------------------------<br>
<br>
Message: 3<br>
Date: Tue, 25 Nov 2014 15:14:38 -0500<br>
From: Fotis Drakopoulos <<a href="mailto:fdrakopo@gmail.com">fdrakopo@gmail.com</a>><br>
To: Bradley Lowekamp <<a href="mailto:blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a>><br>
Cc: "<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>" <<a href="mailto:insight-users@itk.org">insight-users@itk.org</a>>,<br>
"<a href="mailto:insight-developers@itk.org">insight-developers@itk.org</a>" <<a href="mailto:insight-developers@itk.org">insight-developers@itk.org</a>><br>
Subject: Re: [ITK] [ITK-users] Problem reading a big nifti volume.<br>
Message-ID:<br>
<<a href="mailto:CAG6AjRNaVdcxH1ScfVx-k3dXx8i2obffjvtLRvvLqPG1xnCSaA@mail.gmail.com">CAG6AjRNaVdcxH1ScfVx-k3dXx8i2obffjvtLRvvLqPG1xnCSaA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi all,<br>
<br>
I created a test nifti image that reproduces the problem I mentioned 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 <<a href="mailto:blowekamp@mail.nih.gov">blowekamp@mail.nih.gov</a>><br>
wrote:<br>
<br>
> Shareable test data greatly helps determine the cause and fix these 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">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">insight-users-bounces@itk.org</a>] on behalf of Fotis<br>
> Drakopoulos [<a href="mailto:fdrakopo@gmail.com">fdrakopo@gmail.com</a>]<br>
> *Sent:* Monday, 24 November 2014 10:51 a.m.<br>
> *To:* <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>
> *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) 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. So far no problems. The specs of the image on Slicer are the same<br>
> as above (except the direction which has flipped signs for the first two<br>
> diagonal 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 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 specks<br>
> and were the same with the original image as above. However I noticed that<br>
> a big portion of the image is completely empty (black)!<br>
><br>
> My workstation has enough memory to load the image (768 GB 1600MHz 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 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>
> <<a href="https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=s" target="_blank">https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=s</a>><br>
> Not spam<br>
> <<a href="https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=n" target="_blank">https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=n</a>><br>
> Forget previous vote<br>
> <<a href="https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=f" target="_blank">https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=f</a>><br>
><br>
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_____________________________________<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>
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Follow this link to subscribe/unsubscribe:<br>
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End of Community Digest, Vol 14, Issue 72<br>
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<br>
The information in this e-mail is intended only for the person to whom it is<br>
addressed. If you believe this e-mail was sent to you in error and the e-mail<br>
contains patient information, please contact the Partners Compliance HelpLine at<br>
<a href="http://www.partners.org/complianceline" target="_blank">http://www.partners.org/complianceline</a> . If the e-mail was sent to you in error<br>
but does not contain patient information, please contact the sender and properly<br>
dispose of the e-mail.<br>
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