Hello Everyone!

I have several structural images were too much dura was included into the wm calculation. (see recon-all_std for the standard processing image)

I followed the skull strip instructions https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview 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.

This is output to screen and command that I used

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

Thank you!