On Sunday, April 20, 2014 2:25 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
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
> <fis...@nmr.mgh.harvard.edu> 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
> > <shahrzad_k...@yahoo.com> 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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