I'm running a normal brain through FSv5.0.0 using the -cw256 flag and encounter a problem at the mri_normalize stage. The nu.mgz file looks fine...WM regions have intensity values >110; cortical GM regions have intensity values 70-106; csf intensity values are around 60. The output file (T1.mgz) is all black (no different when changing intensity/contrast display options). I tried a "kinder gentler" normalization to write out a T1_gentler.mgz file, but got the same result (all black output image). I see that the # of peaks is not >1 (MRIsplineNormalize)...but not sure how to intervene at this stage.
Any ideas? Many Thanks, Jenifer
[jjuranek@localhost subjects]$ mri_normalize -gentle ATIS_0009_B_cw256/mri/nu.mgz ATIS_0009_B_cw256/mri/T1_gentle.mgz performing kinder gentler normalization... reading from ATIS_0009_B_cw256/mri/nu.mgz... normalizing image... talairach transform 1.081 -0.071 0.112 -2.139; 0.079 1.020 0.075 -20.692; -0.117 -0.062 1.133 -11.092; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRIsplineNormalize(): npeaks = 1 ERROR: number of peaks must be > 1 for spline 1d normalization failed - trying no1d... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to ATIS_0009_B_cw256/mri/T1_gentle.mgz 3D bias adjustment took 0 minutes and 42 seconds.
Hi Jenifer,
I just fixed this bug in 5.1. Does this subject have a lot of damaged white matter? You can download a dev version of mri_normalize or wait for 5.1
cheers Bruce
On Thu, 17 Mar 2011, Juranek, Jenifer wrote:
I'm running a normal brain through FSv5.0.0 using the -cw256 flag and encounter a problem at the mri_normalize stage. The nu.mgz file looks fine...WM regions have intensity values >110; cortical GM regions have intensity values 70-106; csf intensity values are around 60. The output file (T1.mgz) is all black (no different when changing intensity/contrast display options). I tried a "kinder gentler" normalization to write out a T1_gentler.mgz file, but got the same result (all black output image). I see that the # of peaks is not >1 (MRIsplineNormalize)...but not sure how to intervene at this stage.
Any ideas? Many Thanks, Jenifer
[jjuranek@localhost subjects]$ mri_normalize -gentle ATIS_0009_B_cw256/mri/nu.mgz ATIS_0009_B_cw256/mri/T1_gentle.mgz performing kinder gentler normalization... reading from ATIS_0009_B_cw256/mri/nu.mgz... normalizing image... talairach transform 1.081 -0.071 0.112 -2.139; 0.079 1.020 0.075 -20.692; -0.117 -0.062 1.133 -11.092; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRIsplineNormalize(): npeaks = 1 ERROR: number of peaks must be > 1 for spline 1d normalization failed - trying no1d... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to ATIS_0009_B_cw256/mri/T1_gentle.mgz 3D bias adjustment took 0 minutes and 42 seconds. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Bruce Fischl -
Juranek, Jenifer