View Issue Details

Jump to NotesJump to History
IDProjectCategoryView StatusDate SubmittedLast Update
0004143Slicer4Core: Base Codepublic2016-01-29 14:112020-02-18 09:38
Reporterzhangfanmark Assigned ToSunderlandkyl  
PrioritynormalSeveritymajorReproducibilityalways
Status assignedResolutionopen 
PlatformMacOSOS Version
Product VersionSlicer 4.5.0-1 
Target VersionSlicer 4.11.0Fixed in Version 
Summary0004143: Freesurfer surface is not aligned to the MR volume
Description

Dear all,

For the freesurfer outputs, the surface model loaded in Slicer is not aligned to the MR volume. A similar issue has been reported before (http://na-mic.org/Bug/view.php?id=2422), but it is still in the latest version of Slicer.

Also, after loading the surface model and a Scalar Overlay file of the surface parcellation, Slicer can visualize them correctly, but it cannot save the overlaid model.

Attached please find a screenshot related to the issues. Could anyone help check them?
The data for freesurfer tutorial (Slicer3) could be used to see the issues (http://www.na-mic.org/Wiki/index.php/File:FreeSurferTutorialData.zip).

Thanks,
Fan

TagsNo tags attached.

Relationships

related to 0003684 closednicole Unable to save and reopen Freesurfer surface models and scalar overlays using .mrml scene file 

Activities

zhangfanmark

zhangfanmark

2016-01-29 14:11

reporter  

Screen Shot 2016-01-29 at 2.00.11 PM.png (391,808 bytes)
lassoan

lassoan

2017-06-14 17:04

developer   ~0014841

Overlaid model cannot be saved issue is fixed in r26092.
lassoan

lassoan

2017-06-14 17:05

developer   ~0014842

Misalignment issue is still there in nightly version (Slicer 4.7.0-2017-05-27).
lassoan

lassoan

2020-02-17 20:34

developer   ~0016310

Kyle Sunderland developed a Freesurfer importer (https://github.com/Sunderlandkyl/SlicerFSImporter), which fixes this issue, which is caused by FreeSurfer's very questionable choices in defining coordinate systems. All FreeSurfer import classes should be moved into this new extension.

Issue History

Date Modified Username Field Change
2016-01-29 14:11 zhangfanmark New Issue
2016-01-29 14:11 zhangfanmark Status new => assigned
2016-01-29 14:11 zhangfanmark Assigned To => jcfr
2016-01-29 14:11 zhangfanmark File Added: Screen Shot 2016-01-29 at 2.00.11 PM.png
2016-03-01 10:09 nicole Relationship added related to 0003684
2017-06-14 17:04 lassoan Summary Freesurfer surface is not aligned to the MR volume and the overlaid model cannot be saved => Freesurfer surface is not aligned to the MR volume
2017-06-14 17:04 lassoan Note Added: 0014841
2017-06-14 17:05 lassoan Note Added: 0014842
2018-05-30 00:37 lassoan Target Version => backlog
2020-02-17 20:34 lassoan Target Version backlog => Slicer 4.11.0
2020-02-17 20:34 lassoan Note Added: 0016310
2020-02-18 09:38 lassoan Assigned To jcfr => Sunderlandkyl