Thanks, Bruce.  
I pasted the mri_segment and mris_make_surfaces I found in three subjects’ logs.
Expert opts would be -seg-wlo and -seg-ghi? Which values would be reasonable? 
Do they depend on scanning characteristics or do you have a sort of standard 
parameters for the software?
Regards,
Pedro Rosa.

Subject 1:  
#@# WM Segmentation Mon Feb 16 09:08:56 BRST 2015
\n mri_segment brain.mgz wm.seg.mgz \n
doing initial intensity segmentation...
using local statistics to label ambiguous voxels...
computing class statistics for intensity windows...
WM (104.0): 105.0 +- 4.5 [80.0 --> 125.0]
GM (72.0) : 70.1 +- 13.5 [30.0 --> 96.0]
setting bottom of white matter range to 83.6
setting top of gray matter range to 97.1

Subject 2:
WM (105.0): 105.6 +- 4.6 [80.0 --> 125.0]
GM (70.0) : 68.4 +- 13.5 [30.0 --> 96.0]
setting bottom of white matter range to 81.9
setting top of gray matter range to 95.4


Subject 3:
WM (105.0): 105.6 +- 4.3 [80.0 --> 125.0]
GM (71.0) : 69.2 +- 13.9 [30.0 --> 96.0]
setting bottom of white matter range to 83.2
setting top of gray matter range to 97.1


——  

Subject 1:
\n mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs Subject2 lh 
\n
only generating white matter surface
not using aparc to prevent surfaces crossing the midline
INFO: assuming MGZ format for volumes.
using brain.finalsurfs as T1 volume...
$Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $
$Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $
reading volume 
/Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/mri/filled.mgz...
reading volume 
/Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/mri/brain.finalsurfs.mgz...
reading volume /Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/mri/wm.mgz...
14199 bright wm thresholded.
1723 bright non-wm voxels segmented.
reading original surface position from 
/Users/pedrogomesrosa/Desktop/Thin-rerun/Subject2/surf/lh.orig...
computing class statistics...
border white:    347738 voxels (2.07%)
border gray      336007 voxels (2.00%)
WM (95.0): 96.2 +- 6.5 [70.0 --> 110.0]
GM (85.0) : 81.4 +- 13.2 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 57.8 (was 70)
setting MAX_BORDER_WHITE to 105.5 (was 105)
setting MIN_BORDER_WHITE to 71.0 (was 85)
setting MAX_CSF to 44.5 (was 40)
setting MAX_GRAY to 92.5 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 64.4 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 31.3 (was 40)

Subject 2:
setting MIN_GRAY_AT_WHITE_BORDER to 70.2 (was 70)
setting MAX_BORDER_WHITE to 106.6 (was 105)
setting MIN_BORDER_WHITE to 84.0 (was 85)
setting MAX_CSF to 56.4 (was 40)
setting MAX_GRAY to 93.4 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 77.1 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 42.5 (was 40)

Subject 3:
WM (97.0): 97.9 +- 6.2 [70.0 --> 110.0]
GM (87.0) : 83.8 +- 13.5 [30.0 --> 110.0]
setting MIN_GRAY_AT_WHITE_BORDER to 71.5 (was 70)
setting MAX_BORDER_WHITE to 107.2 (was 105)
setting MIN_BORDER_WHITE to 85.0 (was 85)
setting MAX_CSF to 57.9 (was 40)
setting MAX_GRAY to 94.8 (was 95)
setting MAX_GRAY_AT_CSF_BORDER to 78.2 (was 75)
setting MIN_GRAY_AT_CSF_BORDER to 44.4 (was 40)





On Wednesday, February 18, 2015 at 7:58 PM, Bruce Fischl wrote:

> can you check mri_segmet and mris_make_surfaces and see if the  
> auto-detected intensity parameters are reasonable? Things like max gray  
> at csf border and such. If not, you can set them explicitly using the  
> expert opts - this usually works
> Bruce
> On Wed, 18 Feb 2015, Pedro Rosa - Gmail  
> wrote:
>  
> > Hi,
> > I am resending it once I could not find it in the archives.
> > Thanks,
> > Pedro.
> >  
> > Dear Freesurfers,
> > I am working on a 1.5T MPRAGE sample of first-episode psychosis and 
> > controls, and have found that some subjects end up having thin cortical 
> > surfaces with frequent unsegmented deep sulci. I think this was worse with 
> > FreeSurfer 5.3 than with FreeSurfer 5.1. I attached some screen shots of 
> > aparc+aseg labeling T1.mgz from a few of these subjects.
> > This seems to be a widespread cortical issue, although it was heterogeneous 
> > across subjects (some of them seemed to have the “caudal half" of both 
> > hemispheres adequately segmented), and trying to simply rerun those 
> > subjects was not very helpful. Should I manually work on them, rerun 
> > recon-all with distinct parameters, or just discard them?
> > Regards,
> > Pedro Rosa.
> >  
>  
>  
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