Hello FreeSurfer Developers
I'm attempting to evaluate a segmentation result from CAT12, (sorry) with the Freeview program. For version 1.0 superimposing a gifti surface on top of a nifti volume works beautifully, but with the new version 2.0 the orientation is messed up, for the exact same files (see screenshots in attached jpeg’s). Has anybody else experienced this problem, and could it potentially be caused by recent changes in the minc tools which nifti converter I know have been changed between the two Freeview versions, or are they not used in Freeview.
Best Torben
Torben Ellegaard Lund Associate Professor, PhD Center of Functionally Integrative Neuroscience (CFIN) Aarhus University Aarhus University Hospital Building 10G, 5th floor, room 31 Noerrebrogade 44 8000 Aarhus C Denmark Phone: +45 7846 4380 Fax: +45 7846 4400 http://www.cfin.au.dk http://www.cfin.au.dk/ torbenelund@cfin.au.dk mailto:torbenelund@cfin.au.dk (for official stuff) torbenelund@me.com mailto:torbenelund@me.com (for faster response)
Hi Torben,
Would it be possible to send us the volume and the surface file?
Best, Ruopeng
On Jul 4, 2017, at 3:32 AM, Torben Lund torbenelund@me.com wrote:
Hello FreeSurfer Developers
I'm attempting to evaluate a segmentation result from CAT12, (sorry) with the Freeview program. For version 1.0 superimposing a gifti surface on top of a nifti volume works beautifully, but with the new version 2.0 the orientation is messed up, for the exact same files (see screenshots in attached jpeg’s). Has anybody else experienced this problem, and could it potentially be caused by recent changes in the minc tools which nifti converter I know have been changed between the two Freeview versions, or are they not used in Freeview.
Best Torben
Torben Ellegaard Lund Associate Professor, PhD Center of Functionally Integrative Neuroscience (CFIN) Aarhus University Aarhus University Hospital Building 10G, 5th floor, room 31 Noerrebrogade 44 8000 Aarhus C Denmark Phone: +45 7846 4380 Fax: +45 7846 4400 http://www.cfin.au.dk http://www.cfin.au.dk/ torbenelund@cfin.au.dk mailto:torbenelund@cfin.au.dk (for official stuff) torbenelund@me.com mailto:torbenelund@me.com (for faster response)
<Freeview1.0.jpg><Freeview2.0.jpg> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
What did you use to conver to gifti? If you used mris_convert, try it with either --to-scanner or --to-tkr
On 07/04/2017 03:32 AM, Torben Lund wrote:
Hello FreeSurfer Developers
I'm attempting to evaluate a segmentation result from CAT12, (sorry) with the Freeview program. For version 1.0 superimposing a gifti surface on top of a nifti volume works beautifully, but with the new version 2.0 the orientation is messed up, for the exact same files (see screenshots in attached jpeg’s). Has anybody else experienced this problem, and could it potentially be caused by recent changes in the minc tools which nifti converter I know have been changed between the two Freeview versions, or are they not used in Freeview.
Best Torben
Torben Ellegaard Lund Associate Professor, PhD Center of Functionally Integrative Neuroscience (CFIN) Aarhus University Aarhus University Hospital Building 10G, 5th floor, room 31 Noerrebrogade 44 8000 Aarhus C Denmark Phone: +45 7846 4380 Fax: +45 7846 4400 http://www.cfin.au.dk http://www.cfin.au.dk/ torbenelund@cfin.au.dk mailto:torbenelund@cfin.au.dk (for official stuff) torbenelund@me.com mailto:torbenelund@me.com (for faster response)
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Douglas N Greve -
Ruopeng Wang -
Torben Lund