Dear Bruce,
see the screenshot in the attachment.
The coords (RAS) are: 2.2 -23.3 35.9.
The subject I have uploaded has this issue on multiple spots. The issue is quite frequent, I have seen similar spots in several other subjects I have checked so far.
Antonin
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Hi Antonin
I'm having trouble parsing your image. Could you:1. Send the voxel coords of the location that you see overlap. 2. Send an image with *only* the two overlapping surfaces on, shown in different colors? thanks Bruce On Fri, 18 Nov 2016, Antonin Skoch wrote: Dear FreeSurfer experts,
I am using HCP pipelines with my custom modifications of FreeSurferHiResWhite.sh (especially to accomodate full-hires reconstruction) to generate white and pial surfaces.
I tested the v6.0 beta mris_make_surfaces binary to hopefully fix some problems with surfaces I found previously with 5.3.0_HCP version. This update helped to fix my problems but I found that with v.6.0 there is a new issue with overlaping pial surfaces in hemispherical region.
This issue is not present in 5.3.0 version of mris_make_surfaces.
My command line is
mris_make_surfaces -nsigma_above 2 -nsigma_below 3 -aseg aseg.hires -filled filled.hires -wm wm.hires -mgz -sdir my_subject_dir -orig white.deformed -nowhite -orig_white white.deformed -orig_pial pial -T2 my_subj/mri/T2w_hires.norm -T1 T1w_hires_norm my_subject_id lh
The previous invocation of mris_make_surfaces in FreeSurferHiResWhite.sh (which does not use T2 refinement): mris_make_surfaces -variablesigma 4 -white NOWRITE -aseg aseg.hires -orig white.deformed -filled filled.hires -wm wm.hires -sdir my_subject_dir -mgz -T1 T1w_hires_norm my_subject_id lh
produces surfaces which do not overlap.
It seems to me that -aseg option of mris_make_surfaces (preventing surfaces to crossing the midline) is not active in case of -T2 refinement.
I also tried to add -white NOWRITE or -cover_seg parameters, but it did not helped either.
See attached screenshot aseg.hires overlaid with surfaces: blue are surfaces without T2 refinement (without interhemispheric overlap), yellow are surfaces after T2 refinement (with interhemispheric overlap).
Attached is also the log file of my mris_make_surfaces -T2 command.
I also uploaded the subject overlapping_surfs.tar.gz to your FTP file exchange server.
Regards,
Antonin Skoch
