Hi! I’m here with a logistical question — we’ve incorporated these steps into a pipeline that uses the area under the curve of source time-courses in surface based clustering. After using the hack and following the 8 listed steps, how do we ensure that we’ve aligned the surface to the anatomical dataset? I’m interested in using SUMA_AlignToExperiment or something along those lines but I want to better understand at which stage/how to accomplish that. Thank you in advance!
Hi-
Kind of overly excited that in the development version (whenever 1.7 releases), you’ll be able to skip the hack and save_as_surface from the source estimate.
The surfaces should be in alignment since you’re providing the surfaces themselves and the data mapped onto the surfaces. After you upscale the low-res to the higher-res surfaces with SurfToSurf:
SurfToSurf -i_gii SUMA/std.60.lh.white.gii \
-i_gii ${1%.gii}_centered.gii \
-dset $2 \
-prefix std.60.
Then you can visualize with:
suma -spec SUMA/std.60.S01_lh.spec -sv SUMA/S01_SurfVol.nii
Load Dset (std.60.S01-lh.time.niml.dset)
This should be nearly identical to how the data looked for time=0 in MNE. From there any AFNI/SUMA program should work to do manipulations or you can do things to the data via Python.
Hello, that is exciting. Thank you for the update, and looking forward to the release!
Just to clarify - the reason your data should be in alignment is that your SUMA directory is made from the same Freesurfer process that MNE used for doing the source modeling!