On Sunday, April 20, 2014 2:25 AM, Bruce Fischl fischl@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 fischl@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_kh_m@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.
Try running mri_normalize first Cheers Bruce
On Apr 19, 2014, at 9:21 PM, shahrzad kharabian shahrzad_kh_m@yahoo.com wrote:
On Sunday, April 20, 2014 2:25 AM, Bruce Fischl fischl@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 fischl@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_kh_m@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.
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shahrzad kharabian