[ITK] [ITK-users] Big tiff file

[Dženan Zukić]

I guess each format needs additional code in the UI, but reading the file
via ITK is almost the same for non-DICOM formats.

On Sun, Oct 22, 2017 at 2:55 PM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:

> About ITKsnap, Richard made me aware that although it is not possible to
> open a TIFF from the GUI (TIFF is not in the list of supported formats
> shown there), it can be opened from the command line:
> > itksnap zzz.tif
> which is very odd.
> ________________________________________
> From: Matt McCormick <matt.mccormick at kitware.com>
> Sent: Monday, 23 October 2017 7:41 a.m.
> To: Gib Bogle
> Cc: Dženan Zukić; Insight-users
> Subject: Re: [ITK-users] Big tiff file
>
> Thanks for the follow-up, Gib.
>
> On Sat, Oct 21, 2017 at 8:39 PM, Gib Bogle <g.bogle at auckland.ac.nz> wrote:
> > I've managed to find the answer to one of my questions, by looking at
> the file header values.  A TIFF file less than 2GB has these 4 header bytes:
> > 49 49 2A 00
> > and over 2GB (BigTIFF) has
> > 49 49 2B 00
> > ITK handles this automatically.
> >
> > I can view the big TIFFs with Fiji (ImageJ), so this is not a bad option
> for displaying the slices.  What I like about Irfanview is that it's very
> light-weight.  ImageJ loads the whole file into memory, which can take some
> time, while Irfanview loads one slice at a time.
> >
> > I am not keen about Slicer - it is a real heavy-weight - and Tomviz is
> very specialised, designed for viewing tomography data, i.e. images in a
> tilt series.
> > ________________________________________
> > From: Matt McCormick <matt.mccormick at kitware.com>
> > Sent: Sunday, 22 October 2017 4:48 a.m.
> > To: Dženan Zukić
> > Cc: Gib Bogle; Insight-users
> > Subject: Re: [ITK-users] Big tiff file
> >
> > Hi,
> >
> > Since ITKv4, support for "BigTiff" was added, so ITK can support TIFF
> > files larger than 4GB.
> >
> > One possible limitation may be the filesystem -- avoid FAT32 formatted
> > filesystem that will run into size limits.
> >
> > The file could be viewed with a number of ITK-supported viewers, e.g.
> >
> > - 3D-Slicer: https://www.slicer.org/
> > - ITK-SNAP: http://www.itksnap.org/
> > - Tomviz: http://www.tomviz.org/
> >
> > HTH,
> > Matt
> >
> > On Sat, Oct 21, 2017 at 11:40 AM, Dženan Zukić <dzenanz at gmail.com>
> wrote:
> >> Hi Gib,
> >>
> >> TIFF is limited to 4GiB. Unless you must use TIFF, better switch to
> >> MetaImage or NRRD.
> >>
> >> Regards,
> >> Dženan
> >>
> >> On Sat, Oct 21, 2017 at 12:08 AM, Gib Bogle <g.bogle at auckland.ac.nz>
> wrote:
> >>>
> >>> Hi,
> >>>
> >>>
> >>> I am joining a stack of 2D tiffs into a 3D tiff, and have run into a
> >>> problem with big files.  When the uncompressed size of the 3D file is
> more
> >>> than 2GB I get an error when I try to view it with Irfanview.  At
> first I
> >>> thought maybe I needed to upgrade from ITK4.8.0, but after installing
> and
> >>> using ITK4.12.2 I see that I have the same issue.  Irfanview says:
> >>>
> >>> "Invalid or unsupported TIF file"
> >>>
> >>> I now suspect that the problem is not ITK-related, rather it is a
> >>> limitation of Irfanview.
> >>>
> >>> I have two questions:
> >>>
> >>>
> >>> Is there a limit on the allowed size of a tiff file?
> >>>
> >>> Is there another program (preferably free) that can open for viewing
> tiff
> >>> files bigger than 2GB?
> >>>
> >>>
> >>> It is useful but not essential for me to be able to view these big 3D
> >>> files.  I will use ITK functions to process the 3D files, and I'm
> assuming
> >>> that any file that ITK can create it can also read.
> >>>
> >>>
> >>> Thanks
> >>>
> >>> Gib
> >>>
> >>>
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> >>
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