I've been playing around with reconstruction at higher resolutions and have been getting some unusual behavior so I decided to do some testing on bert.
I convert bert to 0.7mm isotropic and 366 slices with:
mri_convert -cs 0.7 ~/subjects/bert/mri/orig ~/subjects/bert0.7/mri/orig
Then I fired up recon-all. Bert's surface came out beautifully without doing any manual editing. There are 276,245 nodes in the surface instead of 137,497 when reconstructed at 1.0mm. The inflated surface also looks a bit more convoluted at 0.7mm than at 1.0mm.
However when I tried to recon bert at 0.5, mri_watershed gave some interesting errors:
Skull Stripping Thu Sep 1 19:07:40 EDT 2005 /misc/radium0/adamt/subjects/bert0.5/mri mri_watershed T1 brain
************************************************************ The input file is T1 The output file is 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=252 y=303 z=228 r=259 first estimation of the main basin volume: 73641890 voxels Error w=White Matter =Intensity too high (>240)...valid input ? warning: non-standard value for imnr1 (512, usually 256) in file /misc/radium0/adamt/subjects/bert0.5/mri/T1/COR-.info warning: non-standard value for x (512, usually 256) in file /misc/radium0/adamt/subjects/bert0.5/mri/T1/COR-.info warning: non-standard value for y (512, usually 256) in file /misc/radium0/adamt/subjects/bert0.5/mri/T1/COR-.info warning: non-standard value for thick (0.0005, usually 0.001) in file /misc/radium0/adamt/subjects/bert0.5/mri/T1/COR-.info warning: non-standard value for psiz (0.0005, usually 0.001) in file /misc/radium0/adamt/subjects/bert0.5/mri/T1/COR-.inf o ERROR: mri_watershed exited with non-zero status
Why would resampling to 0.5mm affect white matter intensity?
Thanks, -Adam
--- Adam Thomas adamt@nih.gov Functional MRI Facility, NIMH/NIH/DHHS 10 Center Dr, Room B1D708A Bethesda MD. 20892-1148 Phone:301-402-6351 Fax: 301-402-1370