I am having problems stripping the skull. I am converting DIACOM files into COR. Do you think that it is a problem of convertion? Should I use any extension for mri_convert? I checked the original files and the image seems to be quite Ok (I used MRIConvert and then opened with medx). I will thank you very much any suggestion. Thanks again.
I received this message:
Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/ali/mri/orig /Users/../Volumes/stem/freesurfer/subjects/ali/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/ali/mri/orig... normalizing image... 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 /Users/../Volumes/stem/freesurfer/subjects/ali/mri/T1 3D bias adjustment took 3 minutes and 18 seconds.
Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/ali/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/ali/mri/brain
************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/ali/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/ali/mri/brain If this is incorrect, please exit quickly the program (Ctl-C)
*************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=127 y=79 z=128 r=67 first estimation of the main basin volume: 1304691 voxels Error w=White Matter =Intensity too high (>240)...valid input ?
Command Finished
look at the T1 volume and see if it is correct (i.e. the white matter voxels are all close to 110). It probably isn't, in which case try either removing the talairach transform (as a bad xform breaks the intensity normalization) or manually select some control points in the white matter with tkmedit.
cheers, Bruce
On Mon, 23 Aug 2004, Wan Park wrote:
I am having problems stripping the skull. I am converting DIACOM files into COR. Do you think that it is a problem of convertion? Should I use any extension for mri_convert? I checked the original files and the image seems to be quite Ok (I used MRIConvert and then opened with medx). I will thank you very much any suggestion. Thanks again.
I received this message:
Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/ali/mri/orig /Users/../Volumes/stem/freesurfer/subjects/ali/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/ali/mri/orig... normalizing image... 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 /Users/../Volumes/stem/freesurfer/subjects/ali/mri/T1 3D bias adjustment took 3 minutes and 18 seconds.
Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/ali/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/ali/mri/brain
The input file is /Users/../Volumes/stem/freesurfer/subjects/ali/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/ali/mri/brain If this is incorrect, please exit quickly the program (Ctl-C)
*************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=127 y=79 z=128 r=67 first estimation of the main basin volume: 1304691 voxels Error w=White Matter =Intensity too high (>240)...valid input ?
Command Finished
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Bruce Fischl -
Wan Park