Hi,
I have a project on 7T data. I processed 26 subjects with FreeSurfer6 recon-all with or without the hires flag. The input is MP2RAGE, 0.6 mm^3, bias corrected, skull strip was done despite a slight piece of dura is still present.
For the data processed at native resolution, with the hires flag, I mainly used this: recon-all -subject -i -parallel -expert -hires The expert file indicating only mris_inflate -n 50 As a result, skull strip had to be fixed for 5 subjects (missing brain pieces). Bilateral temporal pole is missing in the reconstructed surfaces in 19 subjects.
For the downsampled data, without the hires flag : recon-all -subject -i -parallel Bilateral temporal pole is missing in the reconstructed surfaces in only 1 subject. Surfaces are way smoother.
I guess such differences between the classic pipeline and the pipeline tuned for hires data are expected. I was just wondering if I was missing something somewhere, some additional options that I would need to tweak, to get better surfaces with the hires data especially in the temporal pole. For now the only things I see that I could do are adding checkpoints or play with this command line: mris_make_surfaces -max_gray_at_csf_border X -max_csf Y
Thank you and best,
Damien