Hi Wan,
check the T1 volume and see if it looks correct (the intensity of the white matter should be close to or equal to 110 everywhere pretty much). Also, look at the talairach.xfm with tmedit->file->load transform for main volume and make sure it looks reasonable.
Bruce
On Fri, 20 Aug 2004, Wan Park wrote:
Hello, my name is Wan Park and I am working at Columbia University.
After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average.
After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message:
Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first
So I go to see the logs and I find this:
/Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/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/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds.
Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain
The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/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=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels
White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ...
MRIstipSkull failed.
Command Finished
Could you tell me what's wrong? Thanks,
Wan Park
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer