Hi, there,
I have a question about the mri_normalize command, I do not want to use conform, so my command line is mri_normalize -g 1 -noconform nu.mgz T1.mgz
I got an error message as:
using max gradient = 1.000 performing kinder gentler normalization... not interpolating and embedding volume to be 256^3... reading from nu.mgz... normalizing image... talairach transform -1.241 0.006 0.133 1.851; 0.087 0.889 0.292 1.071; 0.125 -0.275 0.973 -6.721; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRIsplineNormalize(): npeaks = 3 Starting OpenSpline(): npoints = 3 MRInormGentlyFindControlPoints: unsupported src format 3 MRI3dGentleNormalize failure! mri_ctrl=NULL
Does this mean that I must load a control data? Is there a way that I can use the mri_normalzie command without conform and control data?
Thanks a lot!
Guang
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Hi Guang,
try using it with -no1d. This will skip the stuff that is trying to fit the bias field with a spline. Not sure if it will work in general though, we almost never use it without conforming.
cheers, Bruce
On Sat, 8 Aug 2009, Guang Zeng wrote:
Hi, there,
I have a question about the mri_normalize command, I do not want to use conform, so my command line is mri_normalize -g 1 -noconform nu.mgz T1.mgz
I got an error message as:
using max gradient = 1.000 performing kinder gentler normalization... not interpolating and embedding volume to be 256^3... reading from nu.mgz... normalizing image... talairach transform -1.241 0.006 0.133 1.851; 0.087 0.889 0.292 1.071; 0.125 -0.275 0.973 -6.721; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRIsplineNormalize(): npeaks = 3 Starting OpenSpline(): npoints = 3 MRInormGentlyFindControlPoints: unsupported src format 3 MRI3dGentleNormalize failure! mri_ctrl=NULL
Does this mean that I must load a control data? Is there a way that I can use the mri_normalzie command without conform and control data?
Thanks a lot!
Guang
Get free photo software from Windows Live http://www.windowslive.com/online/photos?ocid=PID23393::T:WLMTAGL:ON:WL:en-U...
Hi, Bruce,
Thanks, I tried -no1d, it does not work. I think now my question is once the original volume is conformed to 256x256x256, and we ran the recon-all command to get the surface data. Is there a way I can use mri_convert the volume back to the original size?
Thanks a lot! Guang
Date: Sat, 8 Aug 2009 13:24:11 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_normalize problem
Hi Guang,
try using it with -no1d. This will skip the stuff that is trying to fit the bias field with a spline. Not sure if it will work in general though, we almost never use it without conforming.
cheers, Bruce
On Sat, 8 Aug 2009, Guang Zeng wrote:
Hi, there,
I have a question about the mri_normalize command, I do not want to use conform, so my command line is mri_normalize -g 1 -noconform nu.mgz T1.mgz
I got an error message as:
using max gradient = 1.000 performing kinder gentler normalization... not interpolating and embedding volume to be 256^3... reading from nu.mgz... normalizing image... talairach transform -1.241 0.006 0.133 1.851; 0.087 0.889 0.292 1.071; 0.125 -0.275 0.973 -6.721; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRIsplineNormalize(): npeaks = 3 Starting OpenSpline(): npoints = 3 MRInormGentlyFindControlPoints: unsupported src format 3 MRI3dGentleNormalize failure! mri_ctrl=NULL
Does this mean that I must load a control data? Is there a way that I can use the mri_normalzie command without conform and control data?
Thanks a lot!
Guang
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mri_vol2vol --mov orig.mgz --targ rawavg.mgz --regheader --o orig-in-rawavg.mgz
should do it
doug
Guang Zeng wrote:
Hi, Bruce,
Thanks, I tried -no1d, it does not work. I think now my question is once the original volume is conformed to 256x256x256, and we ran the recon-all command to get the surface data. Is there a way I can use mri_convert the volume back to the original size?
Thanks a lot! Guang
Date: Sat, 8 Aug 2009 13:24:11 -0400 From: fischl@nmr.mgh.harvard.edu To: freesurfer_zg@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_normalize problem
Hi Guang,
try using it with -no1d. This will skip the stuff that is trying to
fit the
bias field with a spline. Not sure if it will work in general
though, we
almost never use it without conforming.
cheers, Bruce
On Sat, 8 Aug 2009, Guang Zeng wrote:
Hi, there,
I have a question about the mri_normalize command, I do not want
to use conform, so
my command line is mri_normalize -g 1 -noconform nu.mgz T1.mgz
I got an error message as:
using max gradient = 1.000 performing kinder gentler normalization... not interpolating and embedding volume to be 256^3... reading from nu.mgz... normalizing image... talairach transform -1.241 0.006 0.133 1.851; 0.087 0.889 0.292 1.071; 0.125 -0.275 0.973 -6.721; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRIsplineNormalize(): npeaks = 3 Starting OpenSpline(): npoints = 3 MRInormGentlyFindControlPoints: unsupported src format 3 MRI3dGentleNormalize failure! mri_ctrl=NULL
Does this mean that I must load a control data? Is there a way that I can use the mri_normalzie command without
conform and control data?
Thanks a lot!
Guang
Get free photo software from Windows Live
http://www.windowslive.com/online/photos?ocid=PID23393::T:WLMTAGL:ON:WL:en-U...
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Bruce Fischl -
Douglas N Greve -
Guang Zeng