Converting dicom to nrrd

[josiah.m...@cune.org]

I am a beginner in using this, so bear with me. I have loaded dicom images into the 3d slicer, and I have slicerRT and plastimatch both installed. How do I now convert the dicom files to nrrd?

[Sharp, Gregory C.]

Hi,

 

If your files are in directory “my_dir”, you would do this:

 

plastimatch convert --input my_dir --output-img file.nrrd

 

Greg

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[Josiah McAllister]

How am I to do that? Am I supposed to type that into a cmd? I apologize for the questions, which must seem very elementary, but I have no programming experience and am trying to learn as I go.

On Tue, Jun 20, 2017 at 8:56 AM, Sharp, Gregory C. <GCS...@partners.org> wrote:

Hi,

 

If your files are in directory “my_dir”, you would do this:

 

plastimatch convert --input my_dir --output-img file.nrrd

 

Greg

 

From: plast...@googlegroups.com [mailto:plastimatch@googlegroups.com] On Behalf Of josiah.m...@cune.org
Sent: Tuesday, June 20, 2017 9:10 AM
To: Plastimatch
Subject: [Plastimatch] Converting dicom to nrrd

 

I am a beginner in using this, so bear with me. I have loaded dicom images into the 3d slicer, and I have slicerRT and plastimatch both installed. How do I now convert the dicom files to nrrd?

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[Sharp, Gregory C.]

Yes, you would type that at the command prompt.  For the below to work, you would need to either: (a) add the directory containing the plastimatch executable to your path, or (b) use the full path of the executable.

 

If you are not comfortable with using the command prompt, you can convert image types using 3D Slicer or other tools.

 

From: plast...@googlegroups.com [mailto:plast...@googlegroups.com] On Behalf Of Josiah McAllister
Sent: Tuesday, June 20, 2017 9:59 AM
To: plast...@googlegroups.com
Subject: Re: [Plastimatch] Converting dicom to nrrd

 

How am I to do that? Am I supposed to type that into a cmd? I apologize for the questions, which must seem very elementary, but I have no programming experience and am trying to learn as I go.

On Tue, Jun 20, 2017 at 8:56 AM, Sharp, Gregory C. <GCS...@partners.org> wrote:

Hi,

 

If your files are in directory “my_dir”, you would do this:

 

plastimatch convert --input my_dir --output-img file.nrrd

 

Greg

 

From: plast...@googlegroups.com [mailto:plast...@googlegroups.com] On Behalf Of josiah.m...@cune.org
Sent: Tuesday, June 20, 2017 9:10 AM
To: Plastimatch
Subject: [Plastimatch] Converting dicom to nrrd

 

I am a beginner in using this, so bear with me. I have loaded dicom images into the 3d slicer, and I have slicerRT and plastimatch both installed. How do I now convert the dicom files to nrrd?

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[Josiah McAllister]

If I have the plastimatch extension added on 3d slicer, am I able to use that? Or are you referring to another program which is Plastimatch alone?

On Tue, Jun 20, 2017 at 9:08 AM, Sharp, Gregory C. <GCS...@partners.org> wrote:

Yes, you would type that at the command prompt.  For the below to work, you would need to either: (a) add the directory containing the plastimatch executable to your path, or (b) use the full path of the executable.

 

If you are not comfortable with using the command prompt, you can convert image types using 3D Slicer or other tools.

 

From: plast...@googlegroups.com [mailto:plastimatch@googlegroups.com] On Behalf Of Josiah McAllister
Sent: Tuesday, June 20, 2017 9:59 AM
To: plast...@googlegroups.com
Subject: Re: [Plastimatch] Converting dicom to nrrd

 

How am I to do that? Am I supposed to type that into a cmd? I apologize for the questions, which must seem very elementary, but I have no programming experience and am trying to learn as I go.

On Tue, Jun 20, 2017 at 8:56 AM, Sharp, Gregory C. <GCS...@partners.org> wrote:

Hi,

 

If your files are in directory “my_dir”, you would do this:

 

plastimatch convert --input my_dir --output-img file.nrrd

 

Greg

 

From: plast...@googlegroups.com [mailto:plastimatch@googlegroups.com] On Behalf Of josiah.m...@cune.org
Sent: Tuesday, June 20, 2017 9:10 AM
To: Plastimatch
Subject: [Plastimatch] Converting dicom to nrrd

 

I am a beginner in using this, so bear with me. I have loaded dicom images into the 3d slicer, and I have slicerRT and plastimatch both installed. How do I now convert the dicom files to nrrd?

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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

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[Sharp, Gregory C.]

Yes, I thought you were talking about the plastimatch standalone executable. 

 

In 3D Slicer, plastimatch is not used for converting from DICOM, Slicer has a separate mechanism for that.

 

 

From: plast...@googlegroups.com [mailto:plast...@googlegroups.com] On Behalf Of Josiah McAllister
Sent: Tuesday, June 20, 2017 10:11 AM
To: plast...@googlegroups.com
Subject: Re: [Plastimatch] Converting dicom to nrrd

 

If I have the plastimatch extension added on 3d slicer, am I able to use that? Or are you referring to another program which is Plastimatch alone?

 

On Tue, Jun 20, 2017 at 9:08 AM, Sharp, Gregory C. <GCS...@partners.org> wrote:

Yes, you would type that at the command prompt.  For the below to work, you would need to either: (a) add the directory containing the plastimatch executable to your path, or (b) use the full path of the executable.

 

If you are not comfortable with using the command prompt, you can convert image types using 3D Slicer or other tools.

 

From: plast...@googlegroups.com [mailto:plast...@googlegroups.com] On Behalf Of Josiah McAllister
Sent: Tuesday, June 20, 2017 9:59 AM
To: plast...@googlegroups.com
Subject: Re: [Plastimatch] Converting dicom to nrrd

 

How am I to do that? Am I supposed to type that into a cmd? I apologize for the questions, which must seem very elementary, but I have no programming experience and am trying to learn as I go.

On Tue, Jun 20, 2017 at 8:56 AM, Sharp, Gregory C. <GCS...@partners.org> wrote:

Hi,

 

If your files are in directory “my_dir”, you would do this:

 

plastimatch convert --input my_dir --output-img file.nrrd

 

Greg

 

From: plast...@googlegroups.com [mailto:plast...@googlegroups.com] On Behalf Of josiah.m...@cune.org
Sent: Tuesday, June 20, 2017 9:10 AM
To: Plastimatch
Subject: [Plastimatch] Converting dicom to nrrd

 

I am a beginner in using this, so bear with me. I have loaded dicom images into the 3d slicer, and I have slicerRT and plastimatch both installed. How do I now convert the dicom files to nrrd?

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dispose of the e-mail.

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[Josiah McAllister]

If I am trying to convert large datasets from DICOM to nrrd, is it going to be easier to download the plastimatch standalone, or to use the converter on 3D slicer?

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[Yang-Kyun Park]

Hi Josiah,

You can read the step-by-step manual for windows stand-alone users as follows:

http://plastimatch.org/windows_installation.html

What I usually do is, I put my favorite command lines to some notepads or one note,  and whenever I use it, I modify it and copy and paste it to the command prompt (black screen).

The tip is, you should use "paste" using mouse control, rather than Ctrl+V in keyboards.

Hope this helps.

Yang