Hi Bruce, True, I am trying to use Freesurfer skullstripping as a first step to create an input for Brain extraction tool of FSL so as to get in general acceptable extracted brains without changing BET options a lot for different brain. So, what I am doing is as following: I Deoblique anatomical image in AFNI. Then Bring it to FSL friendly orientation (RPI). Then, change the NIFTI format to mgz using mri_convert and then apply mdi_watershed using the command : mri_watershed -atlas mprage_RPI.mgz mprage_skullstrip.mgz
Here is the output of my anatomical scans preprocessing (including the watershed section) !!!! PREPROCESSING ANATOMICAL SCAN!!!! -------------------------------------- deobliquing sub01 anatomical ++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Apr 12 2012) [64-bit] ++ Authored by: RW Cox ++ Processing AFNI dataset mprage.nii.gz + loading and re-writing dataset mprage.nii.gz (./mprage.nii.gz+orig.HEAD in NIFTI storage) ++ 3drefit processed 1 datasets Reorienting sub01 anatomical skull stripping sub01 anatomical mri_convert --in_type nii --out_type mgz --input_volume mprage_RPI.nii --output_volume mprage_cut.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mprage_RPI.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, 1, 0) k_ras = (-0, -0, 1) writing to mprage_cut.mgz...
Mode: Atlas analysis
********************************************************* The input file is mprage_cut.mgz The output file is mprage_skullstrip.mgz conforming input... MRIchangeType: Building histogram
*************************WATERSHED************************** Sorting... first estimation of the COG coord: x=124 y=128 z=125 r=76 first estimation of the main basin volume: 1892714 voxels mri_watershed Error: w=White Matter =Intensity too high (>240)...valid input ? mri_convert -i mprage_skullstrip.mgz -o mprage_orient.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from mprage_skullstrip.mgz... mghRead(/scr/somalia3/HEP_C_total_II/restingstate_analysis/fconscript_preprocessings/HCV_subjects_2mm_Template/sub01/anat/mprage_skullstrip.mgz, -1): could not open file
Error: input image mprage_orient not valid
Thanks, Shahrzad