Try running mri_normalize first
Cheers
Bruce
> On Apr 19, 2014, at 9:21 PM, shahrzad kharabian
> wrote:
>
> On Sunday, April 20, 2014 2:25 AM, Bruce Fischl
> wrote:
> Hi Shahrzad
>
> can you cc the list so that others can answer?
>
> thanks
> Bruce
>
>
> On Sat, 19 Apr 2014, shahrzad kharabian wrote:
>
> > 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 in the previous email.
> >
> > 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_prepr
> > ocessings/HCV_subjects_2mm_Template/sub01/anat/mprage_skullstrip.mgz, -1):
> > could not open file
> >
> > Error: input image mprage_orient not valid
> >
> > Thanks,
> > Shahrzad
> >
> > On Saturday, April 19, 2014 3:43 PM, Bruce Fischl
> > wrote:
> > can you send us the entire output of the command? And perhaps some
> > background? I assume you are trying to use mri_watershed outside of
> > recon-all?
> >
> > On Sat, 19 Apr 2014, shahrzad kharabian wrote:
> >
> > > On Friday, April 18, 2014 11:43 PM, shahrzad kharabian
> > > wrote:
> > > Dear experts,
> > > I have a encountered an Error while doing skull-stripping using freesurfer
> > > on my T1 weighted images, using mri_watershed
> > >
> > > I am using the following command:
> > >
> > > mri_watershed -atlas mprage_RPI.mgz mprage_skullstrip.mgz
> > >
> > > and here is the error:
> > >
> > > mri_watershed Error:
> > > w=White Matter =Intensity too high (>240)...valid input ?
> > >
> > > I checked the images, actualy White matter intensity is around 300 .
> > >
> > > How could I overcome this issue?
> > >
> > > Bests,
> > > S.
> >
> > >
> > >
> > >
> > >
> > >
> > >
> >
> >
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>
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