help > RE: how to change the reference brain for display?
May 16, 2021  12:05 PM | Alfonso Nieto-Castanon - Boston University
RE: how to change the reference brain for display?
Hi Doora,

Another option to create those lh.white/pial files should work purely in PC/Windows which might be worth pursuing would be to use SPM's own CAT12 toolbox to compute these surfaces from a template/reference anatomical file, and then try the scripts in this post to convert the resulting CAT12 files to freesurfer format?

Hope this helps
Alfonso
Originally posted by doora:
Hi!

Thanks, it kinda helps, my only problem is that I have PC and no freesurfer yet (I spent 8 hours to get everything for it on a Win, only to run into a stupid version clash so I have to start over :-D https://askubuntu.com/questions/895897/e...). But now I know what the ultimate goal is, thank you!
Originally posted by Alfonso Nieto-Castanon:
Hi,

That display is using the 3D brain-surface tessellation defined in the files "lh.pial.surf" and "rh.pial.surf" within the conn/utils/surf/ folder.  These two files can be read using the syntax "patch = conn_surf_readsurf(filename)", and they are stored in standard freesurfer "surface" format (e.g. you could simply copy the lh.pial and rh.pial files that would be generated by freesurfer when running it on your preferred template/reference anatomical file)

Hope this helps
Alfonso
Originally posted by doora:
Hi!

Under ROI second level main results (ring or matriix) display, the results are automatically overlaid on a reference brain/glassbrain (pic attached), which I would like to switch for another image, like I am able to do so within the Glass display/conn 3d display/Surfaces/User defined surface. I was trying to find it in the code where this reference brain image is specified but could not find it on my own. Coul you point me in the right direction, please? (conn_20b)

Thanks in advance!

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TitleAuthorDate
doora May 12, 2021
Alfonso Nieto-Castanon May 13, 2021
doora May 16, 2021
RE: how to change the reference brain for display?
Alfonso Nieto-Castanon May 16, 2021
doora May 17, 2021