Hello everyone,

This is the FreeSurfer version that I am using: freesurfer-Darwin-leopard-i686-stable-pub-v4.4.0

1. I am using watershed to perform more aggressive skull stripping but it seems to be not working for me.

Below, I have provided every command I am running to identify the problem:

setenv FREESURFER_HOME /Applications/freesurfer

source $FREESURFER_HOME/SetUpFreeSurfer.csh

cd to correct directory

setenv SUBJECTS_DIR ${PWD}

Before Watershed:

tkmedit 1203/1203 brainmask.mgz -aux T1.mgz –surfs

See attachment- Before_Watershed.png

After Watershed:

recon-all -subjid 1203 -skullstrip -wsthresh 10 -clean-bm -no-wsgcaatlas -no-isrunning

tkmedit 1203 brainmask.mgz -aux T1.mgz -surfs

See attachment- After_Watershed.png

After watershed, skull stripping seems almost worse and it is not respecting the manual edits that I have done either. You can see the manual edits in the Before_Watershed.png file if you zoom in.

2. Which version of FreeSurfer do I need to have to use gcut as it is giving me the following error-

recon-all -skullstrip -clean-bm -gcut -subjid 10

ERROR: Flag -gcut unrecognized.