[ITK] [ITK-dev] ITK Software Guide Printing
Andriy Fedorov
fedorov at bwh.harvard.edu
Tue Nov 25 18:21:57 EST 2014
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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> 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
> >
> >
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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://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:
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> ------------------------------
>
> 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
> >
> >
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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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