probably easier to do the other way around, eg, tkmeditfv subjectname orig.mgz -surfs -ov example_func.nii.gz -reg reg.dat This is a frontend that will run freeview

On 5/14/2019 5:57 AM, Sam W. wrote:

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Thank you Douglas for your response. That's what I thought but wasn't sure. I have another question if you don't mind. I would like to load the wm surfaces as well, and overlay them on top of the mean functional scan. However they are in conformed space whereas my mean functional scan is in functional space. Also there is no :reg sub-option with the -f flag in freeview. So how can I convert the wm surfaces to functional space? Sam

On Tue, May 14, 2019 at 4:11 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> wrote: you have to use the output of mri_label2vol in the freeview command

On 5/13/2019 5:02 PM, Sam W. wrote:

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Hi,

After bbregister, I ran mri_label2vol to convert a segmentation file to native functional space

mri_label2vol --seg s01/mri/aseg.mgz --reg reg.dat --subject s01 --o aseg-in-func.nii --temp example_func.nii

Now I would like to check how well the example_func and aseg file align.

I tried this freeview -v s01/example_func.nii s01/aseg.mgz:colormap=lut:reg=reg.dat but it does not result in a good alignment

Best regards, Sam

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