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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