Problem with drawing gifti contour on nifty volume in Freeview 2.0 but not in 1.0 - with links to files
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 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 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 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)
Dear Ruopeng
I could send you my own files, but this seems to be a generic general problem and could also be visualised with e.g. the canonical nifti gifti templates included with SPM
gifti surface: https://www.dropbox.com/s/ncmfj6llpr7ode4/cortex_20484.surf.gii?dl=0 https://www.dropbox.com/s/ncmfj6llpr7ode4/cortex_20484.surf.gii?dl=0 nifti surface: https://www.dropbox.com/s/msoouju6lepaybu/single_subj_T1.nii?dl=0 https://www.dropbox.com/s/msoouju6lepaybu/single_subj_T1.nii?dl=0
Best Torben
On 4 Jul 2017, at 15.17, 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 (see results here: https://www.dropbox.com/s/lwhonnzy7n2t87x/Freeview1.0.pdf?dl=0 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 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 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)
Dear Ruopeng
I could send you my own files, but this seems to be a generic general problem and could also be visualised with e.g. the canonical nifti gifti templates included with SPM
gifti surface: https://www.dropbox.com/s/ncmfj6llpr7ode4/cortex_20484.surf.gii?dl=0 https://www.dropbox.com/s/ncmfj6llpr7ode4/cortex_20484.surf.gii?dl=0 nifti surface: https://www.dropbox.com/s/msoouju6lepaybu/single_subj_T1.nii?dl=0 https://www.dropbox.com/s/msoouju6lepaybu/single_subj_T1.nii?dl=0
Best Torben
On 4 Jul 2017, at 15.17, Torben Lund <torbenelund@me.com mailto: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 (see results here: https://www.dropbox.com/s/lwhonnzy7n2t87x/Freeview1.0.pdf?dl=0 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 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 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)
freesurfer@nmr.mgh.harvard.edu
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Torben Lund