I followed the skull strip instructions and the gcut procedure made only minor changes, and so I used the watershed and lowered the threshold it removed the dura, but did not update the .pial files to match the updated edge.

recon-all -skullstrip -wsthresh 20 -clean-bm -subjid 31313422_15544

Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /root/Desktop
Actual FREESURFER_HOME /usr/local/freesurfer
-rwxr-xr-x. 1 root root 1432836 Aug 18 20:19 /root/Desktop/31313422_15544/scripts/recon-all.log
Linux kate.ad.wcas.northwestern.edu 2.6.32-642.3.1.el6.x86_64 #1 SMP Sun Jun 26 18:16:44 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux

 mv -f /root/Desktop/31313422_15544/mri/brainmask.mgz /root/Desktop/31313422_15544/trash

#--------------------------------------------
#@# Skull Stripping Thu Aug 18 20:22:30 CDT 2016
/root/Desktop/31313422_15544/mri

 mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta -h 20 T1.mgz brainmask.auto.mgz


Mode:          T1 normalized volume
Mode:          Use the information of atlas (default parms, --help for details)
Mode:          Preflooding height manually specified

*********************************************************
The input file is T1.mgz
The output file is brainmask.auto.mgz
Weighting the input with atlas information before watershed

*************************WATERSHED**************************
Sorting...
      first estimation of the COG coord: x=125 y=99 z=127 r=92
      first estimation of the main basin volume: 3292184 voxels
      Looking for seedpoints
        2 found in the cerebellum
        18 found in the rest of the brain
      global maximum in x=142, y=84, z=82, Imax=255
      CSF=20, WM_intensity=110, WM_VARIANCE=5
      WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110
      preflooding height equal to 20 percent
done.
Analyze...

      main basin size=24160470213 voxels, voxel volume =1.000
                     = 24160470213 mmm3 = 24160471.040 cm3
done.
PostAnalyze...Basin Prior
 0 basins merged thanks to atlas
      ***** 0 basin(s) merged in 1 iteration(s)
      ***** 0 voxel(s) added to the main basin
done.
Weighting the input with prior template

****************TEMPLATE DEFORMATION****************

      second estimation of the COG coord: x=123,y=102, z=118, r=10759 iterations
^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^

   GLOBAL      CSF_MIN=0, CSF_intensity=9, CSF_MAX=71 , nb = 42714
  RIGHT_CER    CSF_MIN=0, CSF_intensity=10, CSF_MAX=51 , nb = 3276
  LEFT_CER     CSF_MIN=0, CSF_intensity=9, CSF_MAX=42 , nb = 2808
 RIGHT_BRAIN   CSF_MIN=0, CSF_intensity=9, CSF_MAX=76 , nb = 17694
 LEFT_BRAIN    CSF_MIN=0, CSF_intensity=4, CSF_MAX=74 , nb = 17946
    OTHER      CSF_MIN=0, CSF_intensity=31, CSF_MAX=52 , nb = 990
  
                     CSF_MAX  TRANSITION  GM_MIN  GM
    GLOBAL    
  before analyzing :    71,      57,        53,   75
  after  analyzing :    44,      57,        57,   61
   RIGHT_CER  
  before analyzing :    51,      53,        55,   80
  after  analyzing :    51,      54,        55,   60
   LEFT_CER   
  before analyzing :    42,      50,        56,   76
  after  analyzing :    42,      54,        56,   59
  RIGHT_BRAIN 
  before analyzing :    76,      57,        51,   75
  after  analyzing :    44,      57,        57,   61
  LEFT_BRAIN  
  before analyzing :    74,      57,        52,   73
  after  analyzing :    43,      57,        57,   61
     OTHER    
  before analyzing :    52,      66,        77,   92
  after  analyzing :    52,      73,        77,   77
      mri_strip_skull: done peeling brain
      highly tesselated surface with 10242 vertices
      matching...75 iterations

*********************VALIDATION*********************
curvature mean = -0.012, std = 0.010
curvature mean = 75.699, std = 8.484

No Rigid alignment: -atlas Mode Off (basic atlas / no registration)
      before rotation: sse = 3.12, sigma = 4.24
      after  rotation: sse = 3.12, sigma = 4.24
Localization of inacurate regions: Erosion-Dilation steps
      the sse mean is  3.19, its var is  3.44  
      before Erosion-Dilatation  0.12% of inacurate vertices
      after  Erosion-Dilatation  0.00% of inacurate vertices
      Validation of the shape of the surface done.
Scaling of atlas fields onto current surface fields

********FINAL ITERATIVE TEMPLATE DEFORMATION********
Compute Local values csf/gray
Fine Segmentation...50 iterations

      mri_strip_skull: done peeling brain

Brain Size = 2108315 voxels, voxel volume = 1.000 mm3
           = 2108315 mmm3 = 2108.315 cm3


******************************
Saving brainmask.auto.mgz
done

 cp brainmask.auto.mgz brainmask.mgz


#------------------------------------------

Started at Thu Aug 18 20:22:28 CDT 2016
Ended   at Thu Aug 18 20:22:49 CDT 2016
#@#%# recon-all-run-time-hours 0.006
recon-all -s 31313422_15544 finished without error at Thu Aug 18 20:22:49 CDT 2016
done