new to itk-snap...some questions

[M Gallagher]

Hello, I'm a new user of ITK-snap and am struggling with it a bit. My
past experience is with mimics and I'm trying to make the conversion
to itk, but having a few issues. If anyone can help, it'd be greatly
appreciated.

-How much computing power do I need? I have a 2.66ghz corei5 mac (osx)
with 16gb of ram and it moves slow, crashes all the time without
warning.

-My file comes in with hundredsof layers, maybe thousands. Is this
normal? How do i delete them all at one time? I'm currently able to
delete them one at a time only. Not too efficient.

-I'm working with DICOM file of a full arm in greyscale. Is there a
format ITK prefers? It's 1400 slices, is this too big?

- Like I mentioned before it crashes way too often to be usable, and
without warning. Is there a way to make files more efficient or things
more stable. Is it better on Windows?


Any input would be greatly appreciated. Thanks in advance.

-Michael

[Sebastián Vanrell]

Hi Michael,

Just wondering, do you really need to work with all the slices at once? or do you just need some of them? 

What is the resolution of each slice?

In my experience as a user, what really makes the difference is the graphics capability of the computer, and of course, to have enough ram to load the images.

Regards

Sebastián

2012/11/18 M Gallagher <mrg...@gmail.com>

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[m g]

Thank you Octavian for your reply. To answer some questions....

Could you please describe what is the
sequence of operations you perform?
I'm manually segmenting slice by slice. Crashes usually occur if I
change screen modes (single to multiple or other way around), at times
when changing tools. No pattern has presented itself yet. Sometimes
the paint brush behaves very erratic. Many different issues.

Can you share some data and describe how you delete one layer?
I'm referring to the segmentation labels, my mistake. My file has so
many labels, is this common? Is there a way to delete all the labels
at once?

How big is the overall file(s set)?
750MB

I hope this helps clarify some things.

Many thanks,

Michael





On Nov 18, 9:49 am, Octavian Soldea <octaviansol...@gmail.com> wrote:
> Hi Michael

>
> On Sunday, November 18, 2012 1:15:47 AM UTC-5, m g wrote:
>
> > Hello, I'm a new user of ITK-snap and am struggling with it a bit. My
> > past experience is with mimics and I'm trying to make the conversion
> > to itk, but having a few issues. If anyone can help, it'd be greatly
> > appreciated.
>
> > -How much computing power do I need? I have a 2.66ghz corei5 mac (osx)
> > with 16gb of ram and it moves slow, crashes all the time without
> > warning.
>

> The computer you have is quite good. Could you please describe what is the
> sequence of operations you perform?

>
> > -My file comes in with hundredsof layers, maybe thousands. Is this
> > normal? How do i delete them all at one time? I'm currently able to
> > delete them one at a time only. Not too efficient.
>

> Can you share some data and describe how you delete one layer?

>
> > -I'm working with DICOM file of a full arm in greyscale. Is there a
> > format ITK prefers? It's 1400 slices, is this too big?
>

> All the formats that can be read are equally convenient, to the best of my
> knowledge. DICOM is good as well.
> About 1400 slices issue, the file (s) can be too big, however it depends on
> the overall size. How big is the overall file(s set)?

>
> > - Like I mentioned before it crashes way too often to be usable, and
> > without warning. Is there a way to make files more efficient or things
> > more stable. Is it better on Windows?
>

> ITK-SNAP is cross platform, however, different issues can appear in
> different operating systems. We must check this for these specific issues
> to give a good answer.

>
>
>
> > Any input would be greatly appreciated. Thanks in advance.
>
> > -Michael
>

> Please provide a bit more information, and will try to give more feedback.
>
> Best regards,
>   Octavian

[m g]

I have broken the file into smaller 200 slice files, works much
better! Thanks to all for the help!

Best regards,

Michael

[m g]

Thanks Sebastian for the reply. I hadn't thought of dividing up the
files into smaller parts. I do need all the information but they don't
need to be all in one file. Will give this a try. the images are
512x512 greyscale, spacing at 0.625mm, 16 bits. Hope this helps.




Many thanks,




Michael