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
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