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IDProjectCategoryView StatusLast Update
0003079Slicer4Core: Base Codepublic2013-04-24 09:46
ReportergregsharpAssigned Tofedorov 
PrioritynormalSeverityminorReproducibilityalways
Status assignedResolutionopen 
Product Version 
Target VersionFixed in Version 
Summary0003079: Semantics of 4D volumes are undefined
Description

Slicer has no way of knowing if a 4D volume is a vector field, an RGB image, a time series, or "something else".

It would be helpful to include metadata in the image header fields to make the volume semantics clear.

TagsNo tags attached.

Activities

jcfr

jcfr

2013-04-18 11:20

administrator   ~0008437

Hi Andriy,
Since you worked on MultiVolume modules, I am assigning this issue to you.
Let me know what you think.
Jc

gregsharp

gregsharp

2013-04-18 12:28

developer   ~0008439

Cross-reference to forum exchange.

http://massmail.spl.harvard.edu/public-archives/slicer-users/2013/006470.html

fedorov

fedorov

2013-04-18 13:57

developer   ~0008444

I think this distinction is handled somewhere in the guts of ArchetypeVolumeReader already. It does not rely on metadata, I think RGB, DF and multivolume are already handled differently. We can add metadata, but these files will be generated by tools other than Slicer, so we will need some heuristic anyway.

I think someone who worked with that part of Slicer would be able to provide a more authoritative comment (e.g., Steve or Jim).

jcfr

jcfr

2013-04-18 14:03

administrator   ~0008445

Reminder sent to: millerjv, pieper

@Steve, @Jim: What is your perspective on the problem discussed here ?

pieper

pieper

2013-04-24 09:35

administrator   ~0008478

The nrrd spec does a nice job of supplying the metainformation needed to interpret the data. Some other formats also have enough information (nifti, for example). Sometimes though there may be multiple valid interpretations and the user will have to pick.

We probably want to define a nhdr fields for our canonical representation for each use case so they can be read back unambiguously. Other formats will just need to be handled with importers or dialogs.

millerjv

millerjv

2013-04-24 09:46

developer   ~0008479

The translation from file representation to Slicer interpretation is pretty complicated. We cleaned it up a good bit last summer which allowed us to introduce a MultiVolumeReader that is really just a subclass of one of the NRRD readers.

  1. We do use nrrd attributes to represent MultiVolumes. And of course NRRD attributes for DWI, DTI, etc.

  2. The issue I usually come against is that Slicer likes to interpret 3 component vector images as RGB. For the DCE MRI case, our introduction of the MultiVolumeReader addressed this.

Issue History

Date Modified Username Field Change
2013-04-18 11:09 gregsharp New Issue
2013-04-18 11:09 gregsharp Status new => assigned
2013-04-18 11:09 gregsharp Assigned To => jcfr
2013-04-18 11:20 jcfr Assigned To jcfr => fedorov
2013-04-18 11:20 jcfr Note Added: 0008437
2013-04-18 12:28 gregsharp Note Added: 0008439
2013-04-18 13:57 fedorov Note Added: 0008444
2013-04-18 14:03 jcfr Note Added: 0008445
2013-04-24 09:35 pieper Note Added: 0008478
2013-04-24 09:46 millerjv Note Added: 0008479