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IDProjectCategoryView StatusLast Update
0004143Slicer4Core: Base Codepublic2018-05-30 00:37
Reporterzhangfanmark Assigned Tojcfr  
Status assignedResolutionopen 
PlatformMacOSOS Version
Product VersionSlicer 4.5.0-1 
Target VersionbacklogFixed in Version 
Summary0004143: Freesurfer surface is not aligned to the MR volume

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 (, 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 (


TagsNo tags attached.


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




2016-01-29 14:11




2017-06-14 17:04

developer   ~0014841

Overlaid model cannot be saved issue is fixed in r26092.



2017-06-14 17:05

developer   ~0014842

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

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