Hi Wan
Try setting a few control points in the white matter of any dimmer areas of the T1 volume, and save them by selecting File --> Save Control Points.
Next, get back to the mri/directory (or if you already there, make sure to move the control.dat file (control points) to SUBJECT_name/tmp/control.dat
From mri/ run your mri_normalize again using:
mri_normalize -no1d -f ../tmp/control.dat orig T1
Check the voxel values of the output -- if they are in the normal range (i.e. WM 90-110 or so, then your skull strip should work.
All of this is assuming the T1 volume has excessively high voxel valuues.
Let me know if this works!
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer