P.S. I realized the mistake I made in the purpose of --no-cortex flag, being smoothing issues. So, is there a way to transfer freesurfer's standard annotations to study-specific custom templates?
Cheers, Sourena On Sat, Aug 18, 2012 at 8:15 PM, Sourena Soheilinezhad < sourena.soheili@gmail.com> wrote:
Hi Bruce Thanks. The problem is solved. Pardon my last question: After creating a study specific template, I try to map every thickness map into the template using surf2surf and also zero the medial wall with "--no-cortex". Does it mean that the native surface is firstly transformed to the standard fsaverage to extract the cortex and medial wall annotations, and then mapped to the study specific template? Is it ok, or there exists a better approach?
Cheers, Sourena
On 8/18/12, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Sourena
the inflated.H is the mean curvature of the inflated surface and can be used to guide initial large-scale alignment. I think it is generated by
the
current recon-all, but Nick can correct me if not. You can create them using mris_curvature
cheers Bruce
On Sat, 18 Aug 2012, Sourena Soheilinezhad wrote:
Hi experts,
I have tried this syntax for making a surface template: mris_make template ?h sphere subj1 subj2 subj3 my_template.tiff
Output is an error saying "Could not read curvature file: ?h.infalted.H"
But searching in the /surf directory for .H file, I have added "-infname white_avg" to the command and it seems to run smoothly. My question is, what is this .H file? Should I safely ignore the default search for inflated.H and keep on using white_avg.H instead? Also, the make_average_surface command gives the same "missing .H file" error but this time there is no -infname parameter to be manipulated.
Thanks in advance, Sourena _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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