Re: [Freesurfer] Problem with drawing gifti contour on nifty volume in Freeview 2.0 but not in 1.0

[Douglas N Greve]

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 
> torbenel...@cfin.au.dk  (for official 
> stuff)
> torbenel...@me.com    (for faster response)
>
>
>
>
>
>
>
>
>
>
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Re: [Freesurfer] Problem with drawing gifti contour on nifty volume in Freeview 2.0 but not in 1.0

[Ruopeng Wang]

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  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 
> torbenel...@cfin.au.dk  (for official stuff)
> torbenel...@me.com (for faster response) 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] Problem with drawing gifti contour on nifty volume in Freeview 2.0 but not in 1.0 - with links to files

[Torben Lund]

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 (see results here: 
https://www.dropbox.com/s/lwhonnzy7n2t87x/Freeview1.0.pdf?dl=0 
 ), but with 
the new version 2.0 the orientation is messed up (see result here: 
https://www.dropbox.com/s/ma6p4batv2cc6w4/Freeview2.0.pdf?dl=0 
 ), for the 
exact same files. 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.


The issue seems to be platform independent and exist for both MacOS 10.12.15 
and linux (Ubuntu 16.04.1 LTS)

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 
torbenel...@cfin.au.dk  (for official stuff)
torbenel...@me.com (for faster response) 









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