Hello, Bruce,

I loaded the brainmask.mgz, it has a bad skull-stripping results with cerebellum  attached.
I tried to fix this problem by adjusting the watershed parameters, but the interesting thing is:

this is the base template subject which is created by the command line recon-all -base base_id -tp subj1 -tp subj2 -all

I am not sure what is next command line I need to use after I fix the skull-stripping problem,

recon-all -base base_id -tp subj1 -tp subj2 -autorecon2
or
recon-all -s  base_id -autorecon2

Thanks!
Guang

From: fischl@nmr.mgh.harvard.edu
To: freesurfer_zg@hotmail.com
Date: Sat, 13 Mar 2010 17:03:05 -0500
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all fails because of mri_label error

What version are you running?



On Mar 13, 2010, at 4:22 PM, Guang Zeng <freesurfer_zg@hotmail.com> wrote:

Hi, there,

recon-all fails because of mri_label error ,  I copied the last few lines of recon-all.log.
Any suggestions?

gca peak Unknown = 0.94427 ( 0)
gca peak Left_Inf_Lat_Vent = 0.26806 (38)
gca peak CSF = 0.21047 (24)
gca peak Left_Accumbens_area = 0.37761 (71)
gca peak Left_VentralDC = 0.15788 (92)
gca peak Left_undetermined = 1.00000 (35)
gca peak Left_vessel = 0.65148 (62)
gca peak Left_choroid_plexus = 0.09084 (48)
gca peak Right_Inf_Lat_Vent = 0.30889 (34)
gca peak Right_Accumbens_area = 0.44316 (77)
gca peak Right_vessel = 0.83418 (60)
gca peak Right_choroid_plexus = 0.10189 (48)
gca peak Fifth_Ventricle = 0.54604 (27)
gca peak WM_hypointensities = 0.14831 (83)
gca peak non_WM_hypointensities = 0.09346 (54)
gca peak Optic_Chiasm = 0.34849 (76)
mri_ca_label GCA sequential renormalization: label 28 not consistently computed.

not using caudate to estimate GM means
setting label Right_VentralDC based on Left_VentralDC = 1.15 x +  0
estimating mean gm scale to be 1.01 x + 0.0
estimating mean wm scale to be 1.00 x + 0.0
estimating mean csf scale to be 1.04 x + 0.0
Left_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7)
Right_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7)
saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
Linux dnode26.mayo.edu 2.6.18-92.1.6.el5 #1 SMP Wed Jun 25 13:45:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Fri Mar 12 19:55:35 CST 2010


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