[ITK] [ITK-dev] ITK Software Guide Printing
Matt McCormick
matt.mccormick at kitware.com
Tue Nov 25 22:49:38 EST 2014
Hi Andriy,
Here is the repository:
http://itk.org/ITKSoftwareGuide.git
More info can be found in the README:
http://itk.org/gitweb?p=ITKSoftwareGuide.git;a=blob;f=README.md;h=eadf34576971b36c6f1c64c9f9590d7194fa4463;hb=HEAD
Thanks for your interest,
Matt
On Tue, Nov 25, 2014 at 6:21 PM, Andriy Fedorov <fedorov at bwh.harvard.edu> wrote:
>
>
> Can someone share the link to the software guide repository? I would be very
> interested to take a look.
>
>
>
> On Tue, Nov 25, 2014 at 3:14 PM, <community-request at itk.org> wrote:
>>
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>> Today's Topics:
>>
>> 1. Re: [ITK-dev] ITK Software Guide Printing (Johnson, Hans J)
>> 2. Re: [ITK-dev] [ITK-users] Problem reading a big nifti volume.
>> (Fotis Drakopoulos)
>> 3. Re: [ITK-users] Problem reading a big nifti volume.
>> (Fotis Drakopoulos)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Tue, 25 Nov 2014 14:55:49 +0000
>> From: "Johnson, Hans J" <hans-johnson at uiowa.edu>
>> To: Matt McCormick <matt.mccormick at kitware.com>
>> Cc: ITK <insight-developers at itk.org>, Christopher Mullins
>> <christopher.mullins at kitware.com>
>> Subject: Re: [ITK] [ITK-dev] ITK Software Guide Printing
>> Message-ID: <3549BA92-5B59-4300-A0B4-7CD41E696A2D at uiowa.edu>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> 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.
>>
>> A new gerri-patch pushed UpdateITKToNear4.7.
>>
>> Hans
>>
>> On Nov 25, 2014, at 7:06 AM, Matt McCormick
>> <matt.mccormick at kitware.com<mailto:matt.mccormick at kitware.com>> wrote:
>>
>> I think we could use some help with any warnings, especially for Book
>> 1. Thank you!
>>
>> On Mon, Nov 24, 2014 at 4:32 PM,
>> <michkapopoff at gmail.com<mailto:michkapopoff at gmail.com>> wrote:
>> Cool :)
>>
>> I see that we have still some errors on the software guide dashboard:
>> warning: Line length too long for LaTeX printing
>>
>> Will Christopher Mullins have time to work on this before printing, or do
>> you need some help
>> to fix the remaining warnings ?
>>
>> Michka
>>
>> On 24 Nov 2014, at 22:26, Matt McCormick
>> <matt.mccormick at kitware.com<mailto:matt.mccormick at kitware.com>> wrote:
>>
>> Hi,
>>
>> We are scheduled to have the ITK Software Guide sent to the printers
>> next week so the physical books will be available for the 4.7 release.
>> Please have any changes reviewed in Gerrit over the next week.
>>
>> Thanks,
>> Matt
>> _______________________________________________
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>> ------------------------------
>>
>> Message: 2
>> Date: Tue, 25 Nov 2014 15:14:38 -0500
>> From: Fotis Drakopoulos <fdrakopo at gmail.com>
>> To: Bradley Lowekamp <blowekamp at mail.nih.gov>
>> Cc: "insight-users at itk.org" <insight-users at itk.org>,
>> "insight-developers at itk.org" <insight-developers at itk.org>
>> Subject: Re: [ITK] [ITK-dev] [ITK-users] Problem reading a big nifti
>> volume.
>> Message-ID:
>>
>> <CAG6AjRNaVdcxH1ScfVx-k3dXx8i2obffjvtLRvvLqPG1xnCSaA at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi all,
>>
>> I created a test nifti image that reproduces the problem I mentioned
>> before.
>> How can I share this image with the ITK community?
>>
>> Best,
>> Fotis Drakopoulos
>>
>>
>> On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp
>> <blowekamp at mail.nih.gov>
>> wrote:
>>
>> > Shareable test data greatly helps determine the cause and fix these
>> > types
>> > of issues.
>> >
>> > Got data?
>> >
>> > Brad
>> > On Nov 23, 2014, at 5:40 PM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
>> >
>> > This is reminiscent of the previous problem with big TIFF images, now
>> > fixed.
>> >
>> > Gib
>> > ------------------------------
>> > *From:* Insight-users [insight-users-bounces at itk.org] on behalf of Fotis
>> > Drakopoulos [fdrakopo at gmail.com]
>> > *Sent:* Monday, 24 November 2014 10:51 a.m.
>> > *To:* insight-users at itk.org; insight-developers at itk.org
>> > *Subject:* [ITK-users] Problem reading a big nifti volume.
>> >
>> > Hi all,
>> >
>> > For the last couple of days I have been trying reading (unsuccessfully)
>> > a
>> > big nifti volume labeled image from my disk.
>> >
>> > The pixel type is unsigned char and the rest specs of the image are:
>> > Size : [1001, 1001, 8345] (in voxels)
>> > Spacing : [0.012, 0.012, 0.012] (in mm)
>> > Origin : [0, 0, 0]
>> > Direction :
>> > 1 0 0
>> > 0 1 0
>> > 0 0 1
>> >
>> > 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 ).
>> >
>> > 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.
>> >
>> > Then I decided to write the loaded image on the disk using the
>> > itk::ImageFileWriter.
>> >
>> > 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)!
>> >
>> > My workstation has enough memory to load the image (768 GB 1600MHz
>> > DDR3L)
>> > and is using Red Hat Enterprise Linux Server 6.5.
>> > The size of the original nifti volume is :
>> >
>> > - 25.7 MB (.nii.gz)
>> > - 8.36 GB (.nii)
>> >
>> > Has anybody experienced similar difficulties trying to load so big
>> > volume
>> > data?
>> >
>> > Best,
>> > Fotis Drakopoulos
>> > CRTC
>> >
>> > _____________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://www.kitware.com/products/protraining.php
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/insight-users
>> >
>> >
>> > ------------------------------
>> >
>> > Spam
>> >
>> > <https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=s>
>> > Not spam
>> >
>> > <https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=n>
>> > Forget previous vote
>> >
>> > <https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=f>
>> >
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> <http://public.kitware.com/pipermail/community/attachments/20141125/6480b0fc/attachment.html>
>> -------------- next part --------------
>> _______________________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-developers
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Tue, 25 Nov 2014 15:14:38 -0500
>> From: Fotis Drakopoulos <fdrakopo at gmail.com>
>> To: Bradley Lowekamp <blowekamp at mail.nih.gov>
>> Cc: "insight-users at itk.org" <insight-users at itk.org>,
>> "insight-developers at itk.org" <insight-developers at itk.org>
>> Subject: Re: [ITK] [ITK-users] Problem reading a big nifti volume.
>> Message-ID:
>>
>> <CAG6AjRNaVdcxH1ScfVx-k3dXx8i2obffjvtLRvvLqPG1xnCSaA at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi all,
>>
>> I created a test nifti image that reproduces the problem I mentioned
>> before.
>> How can I share this image with the ITK community?
>>
>> Best,
>> Fotis Drakopoulos
>>
>>
>> On Mon, Nov 24, 2014 at 10:13 AM, Bradley Lowekamp
>> <blowekamp at mail.nih.gov>
>> wrote:
>>
>> > Shareable test data greatly helps determine the cause and fix these
>> > types
>> > of issues.
>> >
>> > Got data?
>> >
>> > Brad
>> > On Nov 23, 2014, at 5:40 PM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
>> >
>> > This is reminiscent of the previous problem with big TIFF images, now
>> > fixed.
>> >
>> > Gib
>> > ------------------------------
>> > *From:* Insight-users [insight-users-bounces at itk.org] on behalf of Fotis
>> > Drakopoulos [fdrakopo at gmail.com]
>> > *Sent:* Monday, 24 November 2014 10:51 a.m.
>> > *To:* insight-users at itk.org; insight-developers at itk.org
>> > *Subject:* [ITK-users] Problem reading a big nifti volume.
>> >
>> > Hi all,
>> >
>> > For the last couple of days I have been trying reading (unsuccessfully)
>> > a
>> > big nifti volume labeled image from my disk.
>> >
>> > The pixel type is unsigned char and the rest specs of the image are:
>> > Size : [1001, 1001, 8345] (in voxels)
>> > Spacing : [0.012, 0.012, 0.012] (in mm)
>> > Origin : [0, 0, 0]
>> > Direction :
>> > 1 0 0
>> > 0 1 0
>> > 0 0 1
>> >
>> > 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 ).
>> >
>> > 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.
>> >
>> > Then I decided to write the loaded image on the disk using the
>> > itk::ImageFileWriter.
>> >
>> > 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)!
>> >
>> > My workstation has enough memory to load the image (768 GB 1600MHz
>> > DDR3L)
>> > and is using Red Hat Enterprise Linux Server 6.5.
>> > The size of the original nifti volume is :
>> >
>> > - 25.7 MB (.nii.gz)
>> > - 8.36 GB (.nii)
>> >
>> > Has anybody experienced similar difficulties trying to load so big
>> > volume
>> > data?
>> >
>> > Best,
>> > Fotis Drakopoulos
>> > CRTC
>> >
>> > _____________________________________
>> > Powered by www.kitware.com
>> >
>> > Visit other Kitware open-source projects at
>> > http://www.kitware.com/opensource/opensource.html
>> >
>> > Kitware offers ITK Training Courses, for more information visit:
>> > http://www.kitware.com/products/protraining.php
>> >
>> > Please keep messages on-topic and check the ITK FAQ at:
>> > http://www.itk.org/Wiki/ITK_FAQ
>> >
>> > Follow this link to subscribe/unsubscribe:
>> > http://public.kitware.com/mailman/listinfo/insight-users
>> >
>> >
>> > ------------------------------
>> >
>> > Spam
>> >
>> > <https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=s>
>> > Not spam
>> >
>> > <https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=n>
>> > Forget previous vote
>> >
>> > <https://www.spamtrap.odu.edu/canit/b.php?i=01NjreqIw&m=3de3085bbaec&t=20141124&c=f>
>> >
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL:
>> <http://public.kitware.com/pipermail/community/attachments/20141125/6480b0fc/attachment-0001.html>
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>> _____________________________________
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>>
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/insight-users
>>
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>>
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