Inputting slice parameter question

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Inputting slice parameter question

Gold, Maria E L
Hi,
I'm a newbie 3D slicer user. I have jpeg and tiff files which I am trying to convert to dicoms. I think what I need to do it tell 3d slicer what the slice dimensions are in the jpegs before I can convert them, but I am not quite sure how to change them. I found the "slices" option, but all the dimensions are static there. Is there something I am missing? Is there a better way to change the image format? Any help is very much appreciated.

-Eugenia


M. Eugenia L. Gold
Graduate Student
Department of Geoscience
121 Trowbridge Hall
University of Iowa
Iowa City, Iowa USA 52242
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Re: Inputting slice parameter question

madanrao
Hello Maria,

You can try taking a sub-volume and store it as nrrd file.

Hope it helps.

AM Mohan Rao

On Sun, Nov 7, 2010 at 12:07 AM, Gold, Maria E L <[hidden email]> wrote:
Hi,
I'm a newbie 3D slicer user. I have jpeg and tiff files which I am trying to convert to dicoms. I think what I need to do it tell 3d slicer what the slice dimensions are in the jpegs before I can convert them, but I am not quite sure how to change them. I found the "slices" option, but all the dimensions are static there. Is there something I am missing? Is there a better way to change the image format? Any help is very much appreciated.

-Eugenia


M. Eugenia L. Gold
Graduate Student
Department of Geoscience
121 Trowbridge Hall
University of Iowa
Iowa City, Iowa USA 52242
e-mail: [hidden email]
_______________________________________________
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: Inputting slice parameter question

inorton
In reply to this post by Gold, Maria E L
Hi Eugenia,
You can change the dimensions in the Volume module.  Slicer should be able to read tiffs and jpegs directly as long as you know the "slicing" (usually per-file in jpeg but tiffs can be stacked) and the dimensions. No need to convert to dicom after that, though saving as nrrd will make re-reading easier.
Hope that helps,
-Isaiah

On Sat, Nov 6, 2010 at 2:37 PM, Gold, Maria E L <[hidden email]> wrote:
Hi,
I'm a newbie 3D slicer user. I have jpeg and tiff files which I am trying to convert to dicoms. I think what I need to do it tell 3d slicer what the slice dimensions are in the jpegs before I can convert them, but I am not quite sure how to change them. I found the "slices" option, but all the dimensions are static there. Is there something I am missing? Is there a better way to change the image format? Any help is very much appreciated.

-Eugenia


M. Eugenia L. Gold
Graduate Student
Department of Geoscience
121 Trowbridge Hall
University of Iowa
Iowa City, Iowa USA 52242
e-mail: [hidden email]
_______________________________________________
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: Inputting slice parameter question

inorton
Sorry, meant to say that you can change voxel dimensions, not image dims. You have to reslice to do that :)

On Sun, Nov 7, 2010 at 10:08 AM, Isaiah Norton <[hidden email]> wrote:
Hi Eugenia,
You can change the dimensions in the Volume module.  Slicer should be able to read tiffs and jpegs directly as long as you know the "slicing" (usually per-file in jpeg but tiffs can be stacked) and the dimensions. No need to convert to dicom after that, though saving as nrrd will make re-reading easier.
Hope that helps,
-Isaiah


On Sat, Nov 6, 2010 at 2:37 PM, Gold, Maria E L <[hidden email]> wrote:
Hi,
I'm a newbie 3D slicer user. I have jpeg and tiff files which I am trying to convert to dicoms. I think what I need to do it tell 3d slicer what the slice dimensions are in the jpegs before I can convert them, but I am not quite sure how to change them. I found the "slices" option, but all the dimensions are static there. Is there something I am missing? Is there a better way to change the image format? Any help is very much appreciated.

-Eugenia


M. Eugenia L. Gold
Graduate Student
Department of Geoscience
121 Trowbridge Hall
University of Iowa
Iowa City, Iowa USA 52242
e-mail: [hidden email]
_______________________________________________
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: Inputting slice parameter question

Xiaodong Tao-2
In reply to this post by inorton
Hello,

Slicer does load stack of images (in jpeg, tiff, or other ITK supported format). But your images should be ordered and have a number in filename to identify that order. After images are load in you can use the "Info" tab in Volumes module to change "Image Origin" and "Image Spacing".

To export/save the volume, you can do one of the two things:

1.  Ctrl-S to open "Save Scene and Unsaved Data" dialog box; Leave only the image you loaded checked to save; select desired "File Format"; Pick "File Name" and "Data Directory"; click "Save Selected";

2. Use "Converters"->"Create A Dicom  Series" module. Note that this module only generates a set of essential dicom tags. 

Hope this helps.
Xiaodong


On Nov 7, 2010, at 10:08 AM, Isaiah Norton wrote:

Hi Eugenia,
You can change the dimensions in the Volume module.  Slicer should be able to read tiffs and jpegs directly as long as you know the "slicing" (usually per-file in jpeg but tiffs can be stacked) and the dimensions. No need to convert to dicom after that, though saving as nrrd will make re-reading easier.
Hope that helps,
-Isaiah

On Sat, Nov 6, 2010 at 2:37 PM, Gold, Maria E L <[hidden email]> wrote:
Hi,
I'm a newbie 3D slicer user. I have jpeg and tiff files which I am trying to convert to dicoms. I think what I need to do it tell 3d slicer what the slice dimensions are in the jpegs before I can convert them, but I am not quite sure how to change them. I found the "slices" option, but all the dimensions are static there. Is there something I am missing? Is there a better way to change the image format? Any help is very much appreciated.

-Eugenia


M. Eugenia L. Gold
Graduate Student
Department of Geoscience
121 Trowbridge Hall
University of Iowa
Iowa City, Iowa USA 52242
e-mail: [hidden email]
_______________________________________________
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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To unsubscribe: send email to [hidden email] with unsubscribe as the subject


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