I think this is due to the fact that there is some geometry information in our surface format that is probably not present in gii. Ruopeng, can you verify? doug

On 02/20/2014 05:11 PM, Karen Marie Sandø Ambrosen wrote:

Hi again,

When I convert a surface to .gii with mris_convert, it is shifted compared to the original surface when loaded into freeview (see previous mail). Does anyone know how to solve this?

Best, Karen

On 02/18/2014 10:01 AM, Karen Marie Sandø Ambrosen wrote:

...

Hi Freesurfer experts,

I am trying to run tracktography from freesurfer labels using probtrackx2 in fsl. To convert the labels to surfaces I use the label2surf command as recommended on the fslwiki. To use the label2surf command I need to convert the surface, e.g. lh.white into a fsl-compatible format using mris_convert:

mris_convert lh.white lh.white.gii

When I load lh.white and the created lh.white.gii into freeview the two are not aligned. Aren't they suppose to be similar when lh.white.gii is use in the label2surf command? Do I need additional arguments in the mris_convert command?

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