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IDProjectCategoryView StatusLast Update
0001815Slicer4Core: Base Codepublic2013-08-12 03:44
Reporterfinetjul Assigned Tofinetjul  
PrioritylowSeverityfeatureReproducibilityN/A
Status closedResolutionfixed 
Product VersionSlicer 4.0.1 
Target VersionSlicer 4.4.0Fixed in VersionSlicer 4.3.0 
Summary0001815: Add support for MRC files
Description

http://www.insight-journal.org/browse/publication/729

Additional Information

From Brad:

Hello,

I wrote a MRC ImageIO for ITK:

http://www.insight-journal.org/browse/publication/729

With Slicer 3, I was able to compile the ITK image IO library, and use the ITK PluginIO mechanisms, by placing the shared library in the correct path, or setting the ITK_AUTOLOAD_PATH.

This imageIO is included with ITK 4.0+ in the Review directory. When ITK is compiled with Review it will automatically be loaded.

I may have compiled Slicer with ITK 4.0 and thereby enabling mrc io.

I hope the Slicer folk can fill in the details and correct me if needed.

Brad

TagsNo tags attached.

Activities

blowekamp

blowekamp

2012-03-26 07:37

developer   ~0003915

It's not clear what the requested action is for this issue. I see two possibilities:

1) Add support for reading mrc Images to slicer.
2) Verify and/or Document the usage of ITK_AUTOLOAD_PATH with slicer

For 1, when slicer is build with ITKv4, Slicer the mrc ImageIO will automatically be registered and it'll just work. The following should likely be done, when MRCImageIO moves out of ITK review:
1a) Add the .mrc, and .rec file extensions to list of supported volumes in the GUI, the Image IO, does correctly report the supported extensions, so this may be able to be adjusted for the general case by querying the ITK ImageIOs.
1b) Update the Wiki Page

For 2, It would be nice if there was a configuration in the Application Settings for this environment variable. Previously I used a wrapper script to automatically set this variable specifically for Slicer. On OSX the .app, are more challenging to get this working. As this path should be specific for the Slicer version, the preferences is a logic place for is.

blowekamp

blowekamp

2013-07-05 07:40

developer   ~0008867

With the adoption of ITKv4, Slicer can load "mrc" files.

It's not clear to me what this issue is for... perhaps to just add it to the list of files now? or it could be considered resolved.

finetjul

finetjul

2013-07-09 07:34

administrator   ~0008940

I updated the documentation, it is indeed possible to read mrc files as volumes:
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/SlicerApplication/SupportedDataFormat

However, it is not possible to "save" with MRC file format as of now.

finetjul

finetjul

2013-07-18 06:00

administrator   ~0009124

Fixed in r22210

blowekamp

blowekamp

2013-08-12 03:44

developer   ~0009464

Can happily read and write MRC files.

Issue History

Date Modified Username Field Change
2012-03-16 07:15 finetjul New Issue
2012-03-16 07:15 finetjul Status new => assigned
2012-03-16 07:15 finetjul Assigned To => finetjul
2012-03-16 07:15 finetjul Assigned To finetjul =>
2012-03-26 07:37 blowekamp Note Added: 0003915
2012-08-20 08:36 nicole Status assigned => acknowledged
2012-08-21 11:47 jcfr Target Version => Slicer 4.3.0
2013-07-05 07:35 pieper Target Version Slicer 4.3.0 => Slicer 4.4.0
2013-07-05 07:40 blowekamp Note Added: 0008867
2013-07-09 07:34 finetjul Note Added: 0008940
2013-07-18 06:00 finetjul Note Added: 0009124
2013-07-18 06:00 finetjul Status acknowledged => resolved
2013-07-18 06:00 finetjul Fixed in Version => Slicer 4.3.0
2013-07-18 06:00 finetjul Resolution open => fixed
2013-07-18 06:00 finetjul Assigned To => finetjul
2013-08-12 03:44 blowekamp Note Added: 0009464
2013-08-12 03:44 blowekamp Status resolved => closed