JChris.FillionR: /* Where can I find someone to help me use Slicer? */

2017-02-02T15:28:57Z

Where can I find someone to help me use Slicer?

JChris.FillionR at 18:51, 16 November 2015

2015-11-16T18:51:39Z

UpdateBot: Nightly -> 4.5

2015-11-12T22:05:35Z

Nightly -> 4.5

New page

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={{#titleparts: {{PAGENAME}} | | -1 }}=</noinclude><includeonly>
{{#ifeq: {{#titleparts: {{PAGENAME}} | 3 }} | Documentation/{{documentation/version}}/Developers | | ='''User FAQ: {{{1}}}'''=}}
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== What is Slicer ? ==
{{:Documentation/{{documentation/version}}/Slicer}}

== Where can I download Slicer? ==
3DSlicer is available for download by visiting the following link: http://download.slicer.org

== Where can I download older release of Slicer ? ==

Older releases of 3DSlicer are available here: http://slicer.kitware.com/midas3/folder/274

== How to install Slicer ? ==

{{:Documentation/{{documentation/version}}/Slicer/Install}}

==Is Slicer really free?==

Yes, really, truly, free. Not just a free trial. No pro version with all the good stuff. Slicer is free with no strings attached. You can even re-use the code in any way you want with no royalties and you don't even need to ask us for permission. (Of course we're always happy to hear from people who've found slicer interesting).

See [http://www.slicer.org/pages/LicenseText the Slicer License page] for the legal version of this.

==Where can I find someone to help me use Slicer?==

We rely on the community of users and developers to share their expertise.

The [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Slicer users mailing list] can be joined by signing up [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users here], or you can [http://slicer-users.65878.n3.nabble.com/ browse the archives] to check if your question was already answered. Please provide as much detail as possible if you post a question, including full error logs, a workflow on how to duplicate the problem and what publicly accessible data to use in order to duplicate the problem.

If you post to the mailing list, be sure not to include any [http://en.wikipedia.org/wiki/Protected_health_information Protected Health Information (PHI)] or any other data that would get you or anyone else in trouble. However, posting example data can be very important to people who are interested in helping you solve your problems. If you can replicate your question using data from the [[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] or [[Documentation/{{documentation/version}}/Modules/DataStore|Data Store]] modules that's the first choice.

The [[Documentation/Nightly | Users Manual]] gives descriptions for using each module, and you can check out the [[Documentation/Nightly/Training | Training pages]] for in depth tutorials about workflows.

==Can I use slicer for patient care?==

Slicer is intended for research work and ''has no FDA clearances or approvals of any kind''. It is the responsibility of the user to comply with all laws and regulations (and moral/ethical guidelines) when using slicer.

==How to cite Slicer?==
Please cite the Slicer web site (http://www.slicer.org) and the following publications when publishing work that uses or incorporates Slicer.

*Slicer 4
**Fedorov A., Beichel R., Kalpathy-Cramer J., Finet J., Fillion-Robin J-C., Pujol S., Bauer C., Jennings D., Fennessy F., Sonka M., Buatti J., Aylward S.R., Miller J.V., Pieper S., Kikinis R. [http://www.spl.harvard.edu/publications/item/view/2219 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network]. Magnetic Resonance Imaging 2012; July PMID: 22770690.
*Slicer 3
**Pieper S, Lorensen B, Schroeder W, Kikinis R. [http://www.slicer.org/publications/item/view/68 The NA-MIC Kit: ITK, VTK, Pipelines, Grids and 3D Slicer as an Open Platform for the Medical Image Computing Community.] Proceedings of the 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2006; 1:698-701.
**Pieper S, Halle M, Kikinis R. [http://www.slicer.org/publications/item/view/91 3D SLICER.] Proceedings of the 1st IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2004; 1:632-635.
*Slicer 2
**Gering, David T., Arya Nabavi, Ron Kikinis, Noby Hata, Lauren J. O'Donnell, W. Eric L. Grimson, Ferenc A. Jolesz, Peter M. Black, and William M. Wells. [http://www.slicer.org/publications/item/view/156 An integrated visualization system for surgical planning and guidance using image fusion and an open MR.] Journal of Magnetic Resonance Imaging 13, no. 6 (2001): 967-975.
**Gering D, Nabavi A, Kikinis R, Grimson W, Hata N, Everett P, Jolesz F, Wells W. [http://slicer.org/publications/item/view/816 An Integrated Visualization System for Surgical Planning and Guidance using Image Fusion and Interventional Imaging.] Int Conf Med Image Comput Comput Assist Interv. 1999;2:809-819.

== How do I create an account for the Slicer wiki? ==
Please note: You only need an account if you want to edit or add pages.

Follow the Log in->Request Account link from the upper right corner of the slicer wiki page. Once the account request is approved, you will be e-mailed a notification message and the account will be usable at log in.

==Can I install Slicer without administrator rights?==

The most convenient way to install Slicer is to run the installer package (Slicer-{{documentation/currentversion}}....exe) as administrator. However, installation is not necessary, you just need to unpack the files in the installer package and copy them to your user directory or a USB drive and start it by running ''Slicer.exe''.

You can unpack the installation package by one of the following methods:
* Install Slicer on any computer where you have administrator access. All the files that you need to run Slicer are in the C:\Program Files\Slicer... directory.
* Unpack the installation package by using 7zip or using the InstallExplorer plugin in Total commander or FAR manager (http://nsis.sourceforge.net/Can_I_decompile_an_existing_installer). All the Slicer files will be in the $_OUTDIR directory, except Slicer.exe, so you have to copy Slicer.exe into $_OUTDIR and run it from there. You can rename the $_OUTDIR directory and discard all the other directories ($COMMONFILES, $PLUGINSDIR, etc).

==What if I have problems with Slicer installation?==
You can read our guide explaining [[Documentation/{{documentation/version}}/Report_a_problem|how to report a problem]].

==How to uninstall Slicer?==
*On Windows, choose "Uninstall" option from the Start menu.
*On the Mac, remove the Slicer.app file. To clean up settings, remove "~/.config/www.na-mic.org/"
*On Linux, remove the directory where the application is located. To clean up settings, remove "~/.config/NA-MIC/"

See the information about the location of [[Documentation/{{documentation/version}}/SlicerApplication/Settings|Settings]] for all platforms. If the uninstaller is not working on windows you may need to remove the settings manually.

== Where can I find Slicer tutorials? ==
Slicer tutorials associated with the latest {{documentation/currentversion}} stable release are available by visiting the following link: [[Documentation/Nightly/Training|Click Here]].

==I read errors in the logs complaining about memory==

Errors such as “Description: Failed to allocate memory for image.” indicate that you don’t have enough memory space.
This can be a common issue if you run a 32-bit version of Slicer. You cannot expect a 32-bit executable to deal with any moderately complex problem. The [[Documentation/{{documentation/version}}/SlicerApplication/HardwareConfiguration#32_bit_versus_64_bit|recommended solution]] is to download/build/use Slicer in 64-bit mode.

Possible workarounds:
* Use a 64-bit version of Slicer
* You have somewhat more memory if you run the module in a separate process. To do that open [[Documentation/{{documentation/version}}/SlicerApplication/ApplicationSettings#Modules|Edit / Application Settings / Modules]] and check the “Prefer Executable CLIs” option, then restart Slicer.
* Decrease the size and/or resolution of the input and output images
** Consider [[Documentation/{{documentation/version}}/Modules/Crop_Volume|Crop Volume]] to focus on just your area of interest.
** Consider [[Documentation/{{documentation/version}}/Modules/ResampleScalarVectorDWIVolume|ResampleScalarVectorDWIVolume]] or [[Documentation/{{documentation/version}}/Modules/ResampleScalarVolume|ResampleScalarVolume]] increase the sample spacing (decrease the resolution) of your data.

== Which Slicer version should I use: 3.X or 4.X ? ==

In general slicer3 and slicer4 have roughly similar functionality with respect to registration basics. Probably the most important thing to keep in mind is that slicer3 is no longer actively maintained.

Slicer4, on the other hand, has benefited from literally hundreds of bug fixes over the past several years, and typically has better features and much better performance. Also, the nightly builds of slicer4 are now using ITKv4, which has significantly improved registration code. I am told by active users/developers of ITK that ITKv4 should provide significantly better results in many cases. Also, several new registration techniques are being actively developed for slicer4.

Source: http://massmail.spl.harvard.edu/public-archives/slicer-users/2013/006190.html

== What is my HOME folder ? ==

{|width = "100%"
! width="50%" style="border-bottom: 1px solid darkgrey;font-size: 75%;"| Linux or MacOSX
! width="50%" style="border-bottom: 1px solid darkgrey;font-size: 75%;"| Windows
|-
| valign="top" |
Start a terminal.
{{pre2|<nowiki>
$ echo ~
/home/jchris
</nowiki>}}
| valign="top" |

Start Command Prompt (Start Menu -> All Programs -> Accessories -> Command Prompt)
{{pre2|<nowiki>
> echo %userprofile%
C:\Users\jcfr
</nowiki>}}
|}

← Older revision		Revision as of 18:51, 16 November 2015
Line 43:		Line 43:

	==How to cite Slicer?==		==How to cite Slicer?==
−	~~Please cite the Slicer web site (http://www.slicer.org) and the following publications when publishing work that uses or incorporates Slicer.~~

−	*Slicer 4	+	{{:CitingSlicer}}
−	**Fedorov A., Beichel R., Kalpathy-Cramer J., Finet J., Fillion-Robin J-C., Pujol S., Bauer C., Jennings D., Fennessy F., Sonka M., Buatti J., Aylward S.R., Miller J.V., Pieper S., Kikinis R. [http:~~//www.spl.harvard.edu/publications/item/view/2219 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network]. Magnetic Resonance Imaging 2012; July PMID: 22770690.~~
−	*Slicer 3
−	**Pieper S, Lorensen B, Schroeder W, Kikinis R. [http://www.slicer.org/publications/item/view/68 The NA-MIC Kit: ITK, VTK, Pipelines, Grids and 3D Slicer as an Open Platform for the Medical Image Computing Community.] Proceedings of the 3rd IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2006; 1:698-701.
−	**Pieper S, Halle M, Kikinis R. [http://www.slicer.org/publications/item/view/91 3D SLICER.] Proceedings of the 1st IEEE International Symposium on Biomedical Imaging: From Nano to Macro 2004; 1:632-635.
−	*Slicer 2
−	**Gering, David T., Arya Nabavi, Ron Kikinis, Noby Hata, Lauren J. O'Donnell, W. Eric L. Grimson, Ferenc A. Jolesz, Peter M. Black, and William M. Wells. [http://www.slicer.org/publications/item/view/156 An integrated visualization system for surgical planning and guidance using image fusion and an open MR.] Journal of Magnetic Resonance Imaging 13, no. 6 (2001): 967-975.
−	**Gering D, Nabavi A, Kikinis R, Grimson W, Hata N, Everett P, Jolesz F, Wells W. [http://slicer.org/publications/item/view/816 An Integrated Visualization System for Surgical Planning and Guidance using Image Fusion and Interventional Imaging.] Int Conf Med Image Comput Comput Assist Interv. 1999;2:809-819.

@@ Line 31: / Line 31: @@
 We rely on the community of users and developers to share their expertise.
-The [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users Slicer users mailing list] can be joined by signing up [http://massmail.bwh.harvard.edu/mailman/listinfo/slicer-users here], or you can [http://slicer-users.65878.n3.nabble.com/ browse the archives] to check if your question was already answered. Please provide as much detail as possible if you post a question, including full error logs, a workflow on how to duplicate the problem and what publicly accessible data to use in order to duplicate the problem.
+The [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users Slicer users mailing list] can be joined by signing up [http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users here], or you can [http://slicer-users.65878.n3.nabble.com/ browse the archives] to check if your question was already answered. Please provide as much detail as possible if you post a question, including full error logs, a workflow on how to duplicate the problem and what publicly accessible data to use in order to duplicate the problem.
 If you post to the mailing list, be sure not to include any [http://en.wikipedia.org/wiki/Protected_health_information Protected Health Information (PHI)] or any other data that would get you or anyone else in trouble.  However, posting example data can be very important to people who are interested in helping you solve your problems.  If you can replicate your question using data from the [[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] or [[Documentation/{{documentation/version}}/Modules/DataStore|Data Store]] modules that's the first choice.

Documentation/4.5/FAQ/General - Revision history

JChris.FillionR: /* Where can I find someone to help me use Slicer? */

JChris.FillionR at 18:51, 16 November 2015

UpdateBot: Nightly -> 4.5