Try running mri_normalize first Cheers Bruce > On Apr 19, 2014, at 9:21 PM, shahrzad kharabian <shahrzad_k...@yahoo.com> > wrote: > > 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. > > > > > > > > > > > > > > > > > > > > > > > > > > The information in this e-mail is intended only for the person to whom it is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you in > > error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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