visible hman project

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visible hman project

H B
Hello,
 
 
i have download visible human data (abdom) .raw(more than 7 MB for each) and .png(moe than 3MB)  but i couldn't open it with slicer
 
then i convert .png to gracical the size for each one more than 1.5 MB but also i couldn't open it with slicer.
i try ti convert it to .vtk but it is very large for memory (i have one computer 1GB and another 2GB, OS vista 32bit)
 
did any one succesfully open visible human data?How and in which format...
 
Best Regards
 
 H.B
 
 

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Re: visible hman project

Andrey Fedorov
H B,

32bit windows is not the best platform to work with large datasets,
since you are limited to ~2GB of usable RAM. If it is an option for
you, you might have better luck with Slicer build for 64bit linux. If
not, you might try to split your dataset into smaller sections, and
work with them individually.

AF


2010/12/12 H B <[hidden email]>:

> Hello,
>
>
> i have download visible human data (abdom) .raw(more than 7 MB for each) and
> .png(moe than 3MB)  but i couldn't open it with slicer
>
> then i convert .png to gracical the size for each one more than 1.5 MB but
> also i couldn't open it with slicer.
> i try ti convert it to .vtk but it is very large for memory (i have one
> computer 1GB and another 2GB, OS vista 32bit)
>
> did any one succesfully open visible human data?How and in which format...
>
> Best Regards
>
>  H.B
>
>
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email]
> with unsubscribe as the subject
>
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Re: visible hman project

Dimitrios Eftaxiopoulos
In reply to this post by H B
Hello,
I have loaded a VHP data set of .png images in a straightforward manner using
a 64bit Debian unstable + experimental Linux installation and the Slicer 3.6.2
package included in Debian experimental. After loading, the Window/Level and
Threshold entries in the Display tab of the Volumes module had to be adjusted
for viewing the slices and the 3d layout. Also the Spacing entry in the Info
tab  of the Volumes module had to be adjusted.

Regards
Dimitris

On Sunday 12 December 2010 20:04:53 H B wrote:

> Hello,
>
>
> i have download visible human data (abdom) .raw(more than 7 MB for each)
> and .png(moe than 3MB)  but i couldn't open it with slicer
>
> then i convert .png to gracical the size for each one more than 1.5 MB but
> also i couldn't open it with slicer. i try ti convert it to .vtk but it is
> very large for memory (i have one computer 1GB and another 2GB, OS vista
> 32bit)
>
> did any one succesfully open visible human data?How and in which format...
>
> Best Regards
>
>  H.B
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Re: visible hman project

H B
In reply to this post by Andrey Fedorov

 Hi AF,
 
thank you for this information, do you think it will work if i upgread To 4 GB?
 
Regards
H.B
> Date: Sun, 12 Dec 2010 13:20:07 -0500

> Subject: Re: [slicer-users] visible hman project
> From: [hidden email]
> To: [hidden email]
> CC: [hidden email]
>
> H B,
>
> 32bit windows is not the best platform to work with large datasets,
> since you are limited to ~2GB of usable RAM. If it is an option for
> you, you might have better luck with Slicer build for 64bit linux. If
> not, you might try to split your dataset into smaller sections, and
> work with them individually.
>
> AF
>
>
> 2010/12/12 H B <[hidden email]>:
> > Hello,
> >
> >
> > i have download visible human data (abdom) .raw(more than 7 MB for each) and
> > .png(moe than 3MB)  but i couldn't open it with slicer
> >
> > then i convert .png to gracical the size for each one more than 1.5 MB but
> & gt; also i couldn't open it with slicer.
> > i try ti convert it to .vtk but it is very large for memory (i have one
> > computer 1GB and another 2GB, OS vista 32bit)
> >
> > did any one succesfully open visible human data?How and in which format...
> >
> > Best Regards
> >
> >  H.B
> >
> >
> >
> > _______________________________________________
> > slicer-users mailing list
> > [hidden email]
> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> > To unsubscribe: send email to [hidden email]
> > with unsubscribe as the subject
> >

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Re: visible hman project

H B
In reply to this post by Dimitrios Eftaxiopoulos

Hi Dimitris ,
 
good news, but i think i cant get 64 bit. Do you know, i didn't see linux before,  don't know if it is easy to switch to.
and the time is very limited to me, i have to finish my work in this month. thanks a lot.
 
wish you the best
 
H.B
> From: [hidden email]

> To: [hidden email]
> Date: Sun, 12 Dec 2010 20:37:26 +0200
> Subject: Re: [slicer-users] visible hman project
>
> Hello,
> I have loaded a VHP data set of .png images in a straightforward manner using
> a 64bit Debian unstable + experimental Linux installation and the Slicer 3.6.2
> package included in Debian experimental. After loading, the Window/Level and
> Threshold entries in the Display tab of the Volumes module had to be adjusted
> for viewing the slices and the 3d layout. Also the Spacing entry in the Info
> tab of the Volumes module had to be adjusted.
>
> Regards
> Dimitris
>
> On Sunday 12 December 2010 20:04:53 H B wrote:
> > Hello,
> >
> >
> > i have download visible human data (abdom) .raw(more than 7 MB for each)
> > and .png(moe than 3MB) but i couldn't open it with slicer
> >
> > then i convert .png to gracical the size for each one more than 1.5 MB but
> > also i couldn't open it with slicer. i try ti convert it to .vtk but it is
> > very large for memory (i have one computer 1GB and another 2GB, OS vista
> > 32bit)
> >
> > did any one succesfully open visible human data?How and in which format...
> >
> > Best Regards
> >
> > H.B
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject

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Re: visible hman project

Andrey Fedorov
In reply to this post by H B
H B,

I don't think it will help you, see
http://msdn.microsoft.com/en-us/library/aa366778(v=vs.85).aspx

I understand switching to linux may be a big deal, but just fyi, you
can have both windows and linux at the same time
https://help.ubuntu.com/9.10/switching/dualboot.html. Once you have
linux installed, we have 64-bit Slicer pre-built for you to use.

AF


2010/12/12 H B <[hidden email]>:

>
>  Hi AF,
>
> thank you for this information, do you think it will work if i upgread To 4
> GB?
>
> Regards
> H.B
>> Date: Sun, 12 Dec 2010 13:20:07 -0500
>> Subject: Re: [slicer-users] visible hman project
>> From: [hidden email]
>> To: [hidden email]
>> CC: [hidden email]
>>
>> H B,
>>
>> 32bit windows is not the best platform to work with large datasets,
>> since you are limited to ~2GB of usable RAM. If it is an option for
>> you, you might have better luck with Slicer build for 64bit linux. If
>> not, you might try to split your dataset into smaller sections, and
>> work with them individually.
>>
>> AF
>>
>>
>> 2010/12/12 H B <[hidden email]>:
>> > Hello,
>> >
>> >
>> > i have download visible human data (abdom) .raw(more than 7 MB for each)
>> > and
>> > .png(moe than 3MB)  but i couldn't open it with slicer
>> >
>> > then i convert .png to gracical the size for each one more than 1.5 MB
>> > but
>> & gt; also i couldn't open it with slicer.
>> > i try ti convert it to .vtk but it is very large for memory (i have one
>> > computer 1GB and another 2GB, OS vista 32bit)
>> >
>> > did any one succesfully open visible human data?How and in which
>> > format...
>> >
>> > Best Regards
>> >
>> >  H.B
>> >
>> >
>> >
>> > _______________________________________________
>> > slicer-users mailing list
>> > [hidden email]
>> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>> > To unsubscribe: send email to
>> > [hidden email]
>> > with unsubscribe as the subject
>> >
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email]
> with unsubscribe as the subject
>
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Re: visible hman project

pieper
Administrator
In reply to this post by H B
Hi H.B. -

If you downsample the png files you should be able to find a resolution
that works for you - I've had good luck in windows with the batch
options in irfan view.  Here's a tutorial that will give you the basic idea:

http://www.ofzenandcomputing.com/zanswers/1028

Best,
Steve

On 12/12/2010 04:56 PM, H B wrote:

>
> Hi Dimitris ,
>
> good news, but i think i cant get 64 bit. Do you know, i didn't see
> linux before, don't know if it is easy to switch to.
> and the time is very limited to me, i have to finish my work in this
> month. thanks a lot.
>
> wish you the best
>
> H.B
>  > From: [hidden email]
>  > To: [hidden email]
>  > Date: Sun, 12 Dec 2010 20:37:26 +0200
>  > Subject: Re: [slicer-users] visible hman project
>  >
>  > Hello,
>  > I have loaded a VHP data set of .png images in a straightforward
> manner using
>  > a 64bit Debian unstable + experimental Linux installation and the
> Slicer 3.6.2
>  > package included in Debian experimental. After loading, the
> Window/Level and
>  > Threshold entries in the Display tab of the Volumes module had to be
> adjusted
>  > for viewing the slices and the 3d layout. Also the Spacing entry in
> the Info
>  > tab of the Volumes module had to be adjusted.
>  >
>  > Regards
>  > Dimitris
>  >
>  > On Sunday 12 December 2010 20:04:53 H B wrote:
>  > > Hello,
>  > >
>  > >
>  > > i have download visible human data (abdom) .raw(more than 7 MB for
> each)
>  > > and .png(moe than 3MB) but i couldn't open it with slicer
>  > >
>  > > then i convert .png to gracical the size for each one more than 1.5
> MB but
>  > > also i couldn't open it with slicer. i try ti convert it to .vtk
> but it is
>  > > very large for memory (i have one computer 1GB and another 2GB, OS
> vista
>  > > 32bit)
>  > >
>  > > did any one succesfully open visible human data?How and in which
> format...
>  > >
>  > > Best Regards
>  > >
>  > > H.B
>  > _______________________________________________
>  > slicer-users mailing list
>  > [hidden email]
>  > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>  > To unsubscribe: send email to
> [hidden email] with unsubscribe as the
> subject
>
>
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
_______________________________________________
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Re: visible hman project

H B
In reply to this post by Andrey Fedorov
Hi AF,
 
 
Realy good news, but do you think i should format the hardisk because it is 32 bit now and i wont to install 64 bit lunix???
 
> Date: Sun, 12 Dec 2010 17:52:06 -0500

> Subject: Re: [slicer-users] visible hman project
> From: [hidden email]
> To: [hidden email]
> CC: [hidden email]
>
> H B,
>
> I don't think it will help you, see
> http://msdn.microsoft.com/en-us/library/aa366778(v=vs.85).aspx
>
> I understand switching to linux may be a big deal, but just fyi, you
> can have both windows and linux at the same time
> https://help.ubuntu.com/9.10/switching/dualboot.html. Once you have
> linux installed, we have 64-bit Slicer pre-built for you to use.
>
> AF
>
>
> 2010/12/12 H B <[hidden email]>:
> >
> >  Hi AF,
> >
> > thank you for this information, do you think it will work if i upgread To 4
> > GB?
> >
> > Regards
> > H.B
> >> Date: Sun, 12 Dec 2010 13:20: 07 -0500
> >> Subject: Re: [slicer-users] visible hman project
> >> From: [hidden email]
> >> To: [hidden email]
> >> CC: [hidden email]
> >>
> >> H B,
> >>
> >> 32bit windows is not the best platform to work with large datasets,
> >> since you are limited to ~2GB of usable RAM. If it is an option for
> >> you, you might have better luck with Slicer build for 64bit linux. If
> >> not, you might try to split your dataset into smaller sections, and
> >> work with them individually.
> >>
> >> AF
> >>
> >>
> >> 2010/12/12 H B <[hidden email]>:
> >> > Hello,
> >> >
> >> >
> >> > i have download visible human data (abdom) .raw(more than 7 MB for each)
> >> > and
> &g t;> > .png(moe than 3MB)  but i couldn't open it with slicer
> >> >
> >> > then i convert .png to gracical the size for each one more than 1.5 MB
> >> > but
> >> & gt; also i couldn't open it with slicer.
> >> > i try ti convert it to .vtk but it is very large for memory (i have one
> >> > computer 1GB and another 2GB, OS vista 32bit)
> >> >
> >> > did any one succesfully open visible human data?How and in which
> >> > format...
> >> >
> >> > Best Regards
> >> >
> >> >  H.B
> >> >
> >> >
> >> >
> >> > _______________________________________________
> >> > slicer-users mailing list
> >> > [hidden email]
> >> > http://massmail.spl.harvard.edu/mailman/l istinfo/slicer-users
> >> > To unsubscribe: send email to
> >> > [hidden email]
> >> > with unsubscribe as the subject
> >> >
> >
> > _______________________________________________
> > slicer-users mailing list
> > [hidden email]
> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> > To unsubscribe: send email to [hidden email]
> > with unsubscribe as the subject
> >

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Re: visible hman project

H B
In reply to this post by pieper

 
>Hi all,
 
now slicers can open the dataset, but it is black and white as here:
http://www.alhnuf.com/up/pics-gif/upload/uploads/images/alhnufff98abcf15.jpg
 
is there any thing should be done (set any value) in this case?
 
 
Regards,
 
  H.B

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Re: visible hman project

pieper
Administrator
Hi H.B. -

I think that worked for you - the only thing now is that the default
window/level setting (contrast/brightness) don't look good for the color
images.  You need to go to the Volumes->Display tab and adjust them.
Also adjust the spacing to get the 3D proportions correct.

Also, I'm not sure what your next plans are, but you should know that
RGB color images like the visible human aren't supported in slicer for
much other than slice viewing.  Many of the tools only work on grayscale
volumes.

There's no GUI module in slicer to convert rgb to grayscale (probably
there should be) but it's not hard to do by hand.

First use File->Save to write out the color volume into a new file (say
'savededcolor.nrrd' - be sure to set the file type to '.nrrd' in the
save dialog).

The bring up the Tcl Interactor (find it under the Window menu).

In the console, enter this command:

unu project -a 0 -m mean -i savedcolor.nrrd -o newgray.nrrd

(you may need to add a path to where you saved the data - something like
c:/data/savedcolor.nrrd - be sure to use forward slashes, not backslashes).

Then load newgray.nrrd and adjust the window/level as needed.

You will then be able to use the grayscale volume with the Editor and
other slicer tools.  If you create label maps, you can still select the
color image to use as the Bg layer in the slice windows.

Best,
Steve


On 12/13/2010 01:16 AM, H B wrote:

>
>
>  >Hi all,
>
> now slicers can open the dataset, but it is black and white as here:
> http://www.alhnuf.com/up/pics-gif/upload/uploads/images/alhnufff98abcf15.jpg
>
> is there any thing should be done (set any value) in this case?
>
>
> Regards,
>
> H.B
>
>
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
_______________________________________________
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Re: visible hman project

H B
Hi Steve,
 
How could i know pixel size of the oreginal image? it seems like stupid question
 
The Editor didnt work,and when i try to save it save the first image (i choose nrrd).
When i try to open it it gave me error. Could you help? i dont know where is the error in saving(may because it save the first png inly?)
 
About Lunix, untill now i call 3 maintenence shop but they didnt have linux and they dont know how to download it. i will try tomorrow. (i dont want to lose time in download it i have to find some shop to do it)
 
Regards,
 
H.B
 
> Date: Mon, 13 Dec 2010 13:30:30 -0500

> From: [hidden email]
> To: [hidden email]
> Subject: Re: [slicer-users] visible hman project
>
> Hi -
>
> The spacing should be based on the input data - whatever is spec'd at
> the visibile human website. For example if the orignal pixel size was
> .1x.1 mm and the slices were 5mm thick, then if you resized the image
> files to 1/4 of their original size the spacing would be 4x4x5 (these
> are just made up numbers - you'll need to check.
>
> Best of luck,
> Steve
>
>
> On 12/13/2010 01:07 PM, H B wrote:
> > Hi steve,
> >
> > Thank you for your interest in my problem. I have write itk code to
> > convert it to grayscale. and i use resizing program as AF said.then it
> > opened but the editor didnt work with me, i am trying now to save it as
> > nrrd as you sa id.
> > what should i write when adjust the spacing?
> >
> >
> >
> > > Date: Mon, 13 Dec 2010 08:48:01 -0500
> > > From: [hidden email]
> > > To: [hidden email]
> > > CC: [hidden email]
> > > Subject: Re: [slicer-users] visible hman project
> > >
> > > Hi H.B. -
> > >
> > > I think that worked for you - the only thing now is that the default
> > > window/level setting (contrast/brightness) don't look good for the color
> > > images. You need to go to the Volumes->Display tab and adjust them.
> > > Also adjust the spacing to get the 3D proportions correct.
> > >
> > > Also, I'm not sure what your next plans are, but you should know that
> > > RGB color images like the visible human aren't supported in slicer for
> > > much o ther than slice viewing. Many of the tools only work on grayscale
> > > volumes.
> > >
> > > There's no GUI module in slicer to convert rgb to grayscale (probably
> > > there should be) but it's not hard to do by hand.
> > >
> > > First use File->Save to write out the color volume into a new file (say
> > > 'savededcolor.nrrd' - be sure to set the file type to '.nrrd' in the
> > > save dialog).
> > >
> > > The bring up the Tcl Interactor (find it under the Window menu).
> > >
> > > In the console, enter this command:
> > >
> > > unu project -a 0 -m mean -i savedcolor.nrrd -o newgray.nrrd
> > >
> > > (you may need to add a path to where you saved the data - something like
> > > c:/data/savedcolor.nrrd - be sure to use forward slashes, not
> > backslashes).
> > >
> > > Then load newgray.nrrd and adjust the window/level as needed.
> > >
> > > You will then be able to use the grayscale volume with the Editor and
> > > other slicer tools. If you create label maps, you can still select the
> > > color image to use as the Bg layer in the slice windows.
> > >
> > > Best,
> > > Steve
> > >
> > >
> > > On 12/13/2010 01:16 AM, H B wrote:
> > > >
> > > >
> > > > >Hi all,
> > > >
> > > > now slicers can open the dataset, but it is black and white as here:
> > > >
> > http://www.alhnuf.com/up/pics-gif/upload/uploads/images/alhnufff98abcf15.jpg
> > > >
> > > > is there any thing should be done (set any value) in this case?
> > > >
> > > >
> > > > Regards,
> > > >
> > > > H.B
> > > >
> > > >
> > > >
> > > > _______________________________________________
> > > > slicer-users mailing list
> > > > [hidden email]
> > > > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> > > > To unsubscribe: send email to
> > [hidden email] with unsubscribe as the
> > subject

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Re: visible hman project

pieper
Administrator
Hi -

On 12/13/2010 01:59 PM, H B wrote:
> Hi Steve,
>
> How could i know pixel size of the oreginal image? it seems like stupid
> question
>

The pixel spacing is not in the image files for .jpg or .png  - you
should be able to find it on the web page where you originally
downloaded the data.

> The Editor didnt work,and when i try to save it save the first image (i
> choose nrrd).
> When i try to open it it gave me error. Could you help? i dont know
> where is the error in saving(may because it save the first png inly?)
>

Be sure to pick the file type '.nrrd' when saving the data in slicer.

> About Lunix, untill now i call 3 maintenence shop but they didnt have
> linux and they dont know how to download it. i will try tomorrow. (i
> dont want to lose time in download it i have to find some shop to do it)
>

A nice version of linux that is easy to install is available from
ubuntu.com.  But if you are not familiar with linux you may be better
sticking with windows and sorting out the file format issues directly
(they will be the same on linux so they need to be fix one way or the
other).

Best of luck,
Steve

> Regards,
>
> H.B
>
>  > Date: Mon, 13 Dec 2010 13:30:30 -0500
>  > From: [hidden email]
>  > To: [hidden email]
>  > Subject: Re: [slicer-users] visible hman project
>  >
>  > Hi -
>  >
>  > The spacing should be based on the input data - whatever is spec'd at
>  > the visibile human website. For example if the orignal pixel size was
>  > .1x.1 mm and the slices were 5mm thick, then if you resized the image
>  > files to 1/4 of their original size the spacing would be 4x4x5 (these
>  > are just made up numbers - you'll need to check.
>  >
>  > Best of luck,
>  > Steve
>  >
>  >
>  > On 12/13/2010 01:07 PM, H B wrote:
>  > > Hi steve,
>  > >
>  > > Thank you for your interest in my problem. I have write itk code to
>  > > convert it to grayscale. and i use resizing program as AF said.then it
>  > > opened but the editor didnt work with me, i am trying now to save it as
>  > > nrrd as you sa id.
>  > > what should i write when adjust the spacing?
>  > >
>  > >
>  > >
>  > > > Date: Mon, 13 Dec 2010 08:48:01 -0500
>  > > > From: [hidden email]
>  > > > To: [hidden email]
>  > > > CC: [hidden email]
>  > > > Subject: Re: [slicer-users] visible hman project
>  > > >
>  > > > Hi H.B. -
>  > > >
>  > > > I think that worked for you - the only thing now is that the default
>  > > > window/level setting (contrast/brightness) don't look good for
> the color
>  > > > images. You need to go to the Volumes->Display tab and adjust them.
>  > > > Also adjust the spacing to get the 3D proportions correct.
>  > > >
>  > > > Also, I'm not sure what your next plans are, but you should know that
>  > > > RGB color images like the visible human aren't supported in
> slicer for
>  > > > much o ther than slice viewing. Many of the tools only work on
> grayscale
>  > > > volumes.
>  > > >
>  > > > There's no GUI module in slicer to convert rgb to grayscale (probably
>  > > > there should be) but it's not hard to do by hand.
>  > > >
>  > > > First use File->Save to write out the color volume into a new
> file (say
>  > > > 'savededcolor.nrrd' - be sure to set the file type to '.nrrd' in the
>  > > > save dialog).
>  > > >
>  > > > The bring up the Tcl Interactor (find it under the Window menu).
>  > > >
>  > > > In the console, enter this command:
>  > > >
>  > > > unu project -a 0 -m mean -i savedcolor.nrrd -o newgray.nrrd
>  > > >
>  > > > (you may need to add a path to where you saved the data -
> something like
>  > > > c:/data/savedcolor.nrrd - be sure to use forward slashes, not
>  > > backslashes).
>  > > >
>  > > > Then load newgray.nrrd and adjust the window/level as needed.
>  > > >
>  > > > You will then be able to use the grayscale volume with the Editor and
>  > > > other slicer tools. If you create label maps, you can still
> select the
>  > > > color image to use as the Bg layer in the slice windows.
>  > > >
>  > > > Best,
>  > > > Steve
>  > > >
>  > > >
>  > > > On 12/13/2010 01:16 AM, H B wrote:
>  > > > >
>  > > > >
>  > > > > >Hi all,
>  > > > >
>  > > > > now slicers can open the dataset, but it is black and white as
> here:
>  > > > >
>  > >
> http://www.alhnuf.com/up/pics-gif/upload/uploads/images/alhnufff98abcf15.jpg
>  > > > >
>  > > > > is there any thing should be done (set any value) in this case?
>  > > > >
>  > > > >
>  > > > > Regards,
>  > > > >
>  > > > > H.B
>  > > > >
>  > > > >
>  > > > >
>  > > > > _______________________________________________
>  > > > > slicer-users mailing list
>  > > > > [hidden email]
>  > > > > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>  > > > > To unsubscribe: send email to
>  > > [hidden email] with unsubscribe as the
>  > > subject
>
>
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
_______________________________________________
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[hidden email]
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H B
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Re: visible hman project

H B
Hi Steve,
 
You realy help me.
When i was working in itk (converting to grayscale) i found this statement:
The original Visible Male cryosectional
// images are non-interlaced 24-bit RGB pixels with a resolution of
// 2048x1216 pixels by 1871 slices with a physical spacing of
// approximately 0.33 mm in slice and 1.0 mm between slices.
 
(the ftp which i download the dataset dose not contain information -readme.txt-) i will try to find any information through the web site
 
 
Q. When saving , it will save just one file beside mrml? or it should save as many as the dataset?
 
Thanks alot
 
H.B

 
> Date: Mon, 13 Dec 2010 14:14:51 -0500

> From: [hidden email]
> To: [hidden email]
> CC: [hidden email]
> Subject: Re: [slicer-users] visible hman project
>
> Hi -
>
> On 12/13/2010 01:59 PM, H B wrote:
> > Hi Steve,
> >
> > How could i know pixel size of the oreginal image? it seems like stupid
> > question
> >
>
> The pixel spacing is not in the image files for .jpg or .png - you
> should be able to find it on the web page where you originally
> downloaded the data.
>
> > The Editor didnt work,and when i try to save it save the first image (i
> > choose nrrd).
> > When i try to open it it gave me error. Could you help? i dont know
> > where is the error in saving(may because it save the first png inly?)
> >
>
> Be sure to pick the file type '.nrrd' when saving t he data in slicer.
>
> > About Lunix, untill now i call 3 maintenence shop but they didnt have
> > linux and they dont know how to download it. i will try tomorrow. (i
> > dont want to lose time in download it i have to find some shop to do it)
> >
>
> A nice version of linux that is easy to install is available from
> ubuntu.com. But if you are not familiar with linux you may be better
> sticking with windows and sorting out the file format issues directly
> (they will be the same on linux so they need to be fix one way or the
> other).
>
> Best of luck,
> Steve
>
> > Regards,
> >
> > H.B
> >
> > > Date: Mon, 13 Dec 2010 13:30:30 -0500
> > > From: [hidden email]
> > > To: [hidden email]
> > > Subject: Re: [slicer-users] visible hman project
> > >
> > & gt; Hi -
> > >
> > > The spacing should be based on the input data - whatever is spec'd at
> > > the visibile human website. For example if the orignal pixel size was
> > > .1x.1 mm and the slices were 5mm thick, then if you resized the image
> > > files to 1/4 of their original size the spacing would be 4x4x5 (these
> > > are just made up numbers - you'll need to check.
> > >
> > > Best of luck,
> > > Steve
> > >
> > >
> > > On 12/13/2010 01:07 PM, H B wrote:
> > > > Hi steve,
> > > >
> > > > Thank you for your interest in my problem. I have write itk code to
> > > > convert it to grayscale. and i use resizing program as AF said.then it
> > > > opened but the editor didnt work with me, i am trying now to save it as
> > > > nrrd as you sa id.
> > > > what should i write when adjust the spacing?
> > > >
> > > >
> > > >
> > > > > Date: Mon, 13 Dec 2010 08:48:01 -0500
> > > > > From: [hidden email]
> > > > > To: [hidden email]
> > > > > CC: [hidden email]
> > > > > Subject: Re: [slicer-users] visible hman project
> > > > >
> > > > > Hi H.B. -
> > > > >
> > > > > I think that worked for you - the only thing now is that the default
> > > > > window/level setting (contrast/brightness) don't look good for
> > the color
> > > > > images. You need to go to the Volumes->Display tab and adjust them.
> > > > > Also adjust the spacing to get the 3D proportions correct.
> > > > >
> > > > & gt; Also, I'm not sure what your next plans are, but you should know that
> > > > > RGB color images like the visible human aren't supported in
> > slicer for
> > > > > much o ther than slice viewing. Many of the tools only work on
> > grayscale
> > > > > volumes.
> > > > >
> > > > > There's no GUI module in slicer to convert rgb to grayscale (probably
> > > > > there should be) but it's not hard to do by hand.
> > > > >
> > > > > First use File->Save to write out the color volume into a new
> > file (say
> > > > > 'savededcolor.nrrd' - be sure to set the file type to '.nrrd' in the
> > > > > save dialog).
> > > > >
> > > > > The bring up the Tcl Interactor (find it under the Window menu).
> > > > >
> > > ; > > In the console, enter this command:
> > > > >
> > > > > unu project -a 0 -m mean -i savedcolor.nrrd -o newgray.nrrd
> > > > >
> > > > > (you may need to add a path to where you saved the data -
> > something like
> > > > > c:/data/savedcolor.nrrd - be sure to use forward slashes, not
> > > > backslashes).
> > > > >
> > > > > Then load newgray.nrrd and adjust the window/level as needed.
> > > > >
> > > > > You will then be able to use the grayscale volume with the Editor and
> > > > > other slicer tools. If you create label maps, you can still
> > select the
> > > > > color image to use as the Bg layer in the slice windows.
> > > > >
> > > > > Best,
> > > > > Steve
> > > & gt; >
> > > > >
> > > > > On 12/13/2010 01:16 AM, H B wrote:
> > > > > >
> > > > > >
> > > > > > >Hi all,
> > > > > >
> > > > > > now slicers can open the dataset, but it is black and white as
> > here:
> > > > > >
> > > >
> > http://www.alhnuf.com/up/pics-gif/upload/uploads/images/alhnufff98abcf15.jpg
> > > > > >
> > > > > > is there any thing should be done (set any value) in this case?
> > > > > >
> > > > > >
> > > > > > Regards,
> > > > > >
> > > > > > H.B
> > > > > >
> > > > > >
> > > > > >
> > > > > > ____________________________________________ ___
> > > > > > slicer-users mailing list
> > > > > > [hidden email]
> > > > > > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> > > > > > To unsubscribe: send email to
> > > > [hidden email] with unsubscribe as the
> > > > subject
> >
> >
> >
> > _______________________________________________
> > slicer-users mailing list
> > [hidden email]
> > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> > To unsubscribe: send email to [hidden email] with unsubscribe as the subject

_______________________________________________
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Re: visible hman project

pieper
Administrator
yes - that's the info you need about the spacing.

For saving, just select the color image volume and set the type to be
.nrrd and then run the command I sent earlier.  then you can reload the
grayscale volume.

-Steve

On 12/13/2010 02:38 PM, H B wrote:

> Hi Steve,
>
> You realy help me.
> When i was working in itk (converting to grayscale) i found this statement:
> The original Visible Male cryosectional
> // images are non-interlaced 24-bit RGB pixels with a resolution of
> // 2048x1216 pixels by 1871 slices with a physical spacing of
> // approximately 0.33 mm in slice and 1.0 mm between slices.
>
> (the ftp which i download the dataset dose not contain information
> -readme.txt-) i will try to find any information through the web site
>
>
> Q. When saving , it will save just one file beside mrml? or it should
> save as many as the dataset?
>
> Thanks alot
>
> H.B
>
>
>  > Date: Mon, 13 Dec 2010 14:14:51 -0500
>  > From: [hidden email]
>  > To: [hidden email]
>  > CC: [hidden email]
>  > Subject: Re: [slicer-users] visible hman project
>  >
>  > Hi -
>  >
>  > On 12/13/2010 01:59 PM, H B wrote:
>  > > Hi Steve,
>  > >
>  > > How could i know pixel size of the oreginal image? it seems like stupid
>  > > question
>  > >
>  >
>  > The pixel spacing is not in the image files for .jpg or .png - you
>  > should be able to find it on the web page where you originally
>  > downloaded the data.
>  >
>  > > The Editor didnt work,and when i try to save it save the first image (i
>  > > choose nrrd).
>  > > When i try to open it it gave me error. Could you help? i dont know
>  > > where is the error in saving(may because it save the first png inly?)
>  > >
>  >
>  > Be sure to pick the file type '.nrrd' when saving t he data in slicer.
>  >
>  > > About Lunix, untill now i call 3 maintenence shop but they didnt have
>  > > linux and they dont know how to download it. i will try tomorrow. (i
>  > > dont want to lose time in download it i have to find some shop to
> do it)
>  > >
>  >
>  > A nice version of linux that is easy to install is available from
>  > ubuntu.com. But if you are not familiar with linux you may be better
>  > sticking with windows and sorting out the file format issues directly
>  > (they will be the same on linux so they need to be fix one way or the
>  > other).
>  >
>  > Best of luck,
>  > Steve
>  >
>  > > Regards,
>  > >
>  > > H.B
>  > >
>  > > > Date: Mon, 13 Dec 2010 13:30:30 -0500
>  > > > From: [hidden email]
>  > > > To: [hidden email]
>  > > > Subject: Re: [slicer-users] visible hman project
>  > > >
>  > > & gt; Hi -
>  > > >
>  > > > The spacing should be based on the input data - whatever is spec'd at
>  > > > the visibile human website. For example if the orignal pixel size was
>  > > > .1x.1 mm and the slices were 5mm thick, then if you resized the image
>  > > > files to 1/4 of their original size the spacing would be 4x4x5 (these
>  > > > are just made up numbers - you'll need to check.
>  > > >
>  > > > Best of luck,
>  > > > Steve
>  > > >
>  > > >
>  > > > On 12/13/2010 01:07 PM, H B wrote:
>  > > > > Hi steve,
>  > > > >
>  > > > > Thank you for your interest in my problem. I have write itk code to
>  > > > > convert it to grayscale. and i use resizing program as AF
> said.then it
>  > > > > opened but the editor didnt work with me, i am trying now to
> save it as
>  > > > > nrrd as you sa id.
>  > > > > what should i write when adjust the spacing?
>  > > > >
>  > > > >
>  > > > >
>  > > > > > Date: Mon, 13 Dec 2010 08:48:01 -0500
>  > > > > > From: [hidden email]
>  > > > > > To: [hidden email]
>  > > > > > CC: [hidden email]
>  > > > > > Subject: Re: [slicer-users] visible hman project
>  > > > > >
>  > > > > > Hi H.B. -
>  > > > > >
>  > > > > > I think that worked for you - the only thing now is that the
> default
>  > > > > > window/level setting (contrast/brightness) don't look good for
>  > > the color
>  > > > > > images. You need to go to the Volumes->Display tab and adjust
> them.
>  > > > > > Also adjust the spacing to get the 3D proportions correct.
>  > > > > >
>  > > > > & gt; Also, I'm not sure what your next plans are, but you
> should know that
>  > > > > > RGB color images like the visible human aren't supported in
>  > > slicer for
>  > > > > > much o ther than slice viewing. Many of the tools only work on
>  > > grayscale
>  > > > > > volumes.
>  > > > > >
>  > > > > > There's no GUI module in slicer to convert rgb to grayscale
> (probably
>  > > > > > there should be) but it's not hard to do by hand.
>  > > > > >
>  > > > > > First use File->Save to write out the color volume into a new
>  > > file (say
>  > > > > > 'savededcolor.nrrd' - be sure to set the file type to '.nrrd'
> in the
>  > > > > > save dialog).
>  > > > > >
>  > > > > > The bring up the Tcl Interactor (find it under the Window menu).
>  > > > > >
>  > > > ; > > In the console, enter this command:
>  > > > > >
>  > > > > > unu project -a 0 -m mean -i savedcolor.nrrd -o newgray.nrrd
>  > > > > >
>  > > > > > (you may need to add a path to where you saved the data -
>  > > something like
>  > > > > > c:/data/savedcolor.nrrd - be sure to use forward slashes, not
>  > > > > backslashes).
>  > > > > >
>  > > > > > Then load newgray.nrrd and adjust the window/level as needed.
>  > > > > >
>  > > > > > You will then be able to use the grayscale volume with the
> Editor and
>  > > > > > other slicer tools. If you create label maps, you can still
>  > > select the
>  > > > > > color image to use as the Bg layer in the slice windows.
>  > > > > >
>  > > > > > Best,
>  > > > > > Steve
>  > > > & gt; >
>  > > > > >
>  > > > > > On 12/13/2010 01:16 AM, H B wrote:
>  > > > > > >
>  > > > > > >
>  > > > > > > >Hi all,
>  > > > > > >
>  > > > > > > now slicers can open the dataset, but it is black and white as
>  > > here:
>  > > > > > >
>  > > > >
>  > >
> http://www.alhnuf.com/up/pics-gif/upload/uploads/images/alhnufff98abcf15.jpg
>  > > > > > >
>  > > > > > > is there any thing should be done (set any value) in this case?
>  > > > > > >
>  > > > > > >
>  > > > > > > Regards,
>  > > > > > >
>  > > > > > > H.B
>  > > > > > >
>  > > > > > >
>  > > > > > >
>  > > > > > > ____________________________________________ ___
>  > > > > > > slicer-users mailing list
>  > > > > > > [hidden email]
>  > > > > > > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>  > > > > > > To unsubscribe: send email to
>  > > > > [hidden email] with unsubscribe
> as the
>  > > > > subject
>  > >
>  > >
>  > >
>  > > _______________________________________________
>  > > slicer-users mailing list
>  > > [hidden email]
>  > > http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
>  > > To unsubscribe: send email to
> [hidden email] with unsubscribe as the
> subject
>
>
>
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email] with unsubscribe as the subject
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject