Hi Pom

how long has it run? What you are seeing is probably normal. Let it run to completion and see how things look

cheers Bruce On Thu, 4 Sep 2014, Pom Sailasuta wrote:

Hello,

I am using FreeSurfer version 5.3.0  in 64bit desktop,

I got these errors at the begining of recon-all but the reconstruction is not stop, keep on going with lots of invalid=96777.

**************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.849, neg=0, invalid=96777 0001: dt=129.472000, rms=0.789 (7.080%), neg=0, invalid=96777 0002: dt=295.936000, rms=0.765 (3.083%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.759 (0.766%), neg=0, invalid=96777 0004: dt=517.888000, rms=0.749 (1.353%), neg=0, invalid=96777 0005: dt=92.480000, rms=0.744 (0.567%), neg=0, invalid=96777 0006: dt=369.920000, rms=0.740 (0.600%), neg=0, invalid=96777 0007: dt=73.984000, rms=0.738 (0.229%), neg=0, invalid=96777 0008: dt=73.984000, rms=0.737 (0.148%), neg=0, invalid=96777 0009: dt=73.984000, rms=0.735 (0.250%), neg=0, invalid=96777 0010: dt=73.984000, rms=0.733 (0.313%), neg=0, invalid=96777 0011: dt=73.984000, rms=0.730 (0.371%), neg=0, invalid=96777 0012: dt=73.984000, rms=0.727 (0.408%), neg=0, invalid=96777 0013: dt=73.984000, rms=0.724 (0.430%), neg=0, invalid=96777 0014: dt=73.984000, rms=0.721 (0.450%), neg=0, invalid=96777 0015: dt=73.984000, rms=0.718 (0.450%), neg=0, invalid=96777 0016: dt=73.984000, rms=0.714 (0.455%), neg=0, invalid=96777 0017: dt=73.984000, rms=0.711 (0.442%), neg=0, invalid=96777 0018: dt=73.984000, rms=0.708 (0.424%), neg=0, invalid=96777 0019: dt=73.984000, rms=0.705 (0.403%), neg=0, invalid=96777 0020: dt=73.984000, rms=0.703 (0.388%), neg=0, invalid=96777 0021: dt=73.984000, rms=0.700 (0.347%), neg=0, invalid=96777 0022: dt=73.984000, rms=0.698 (0.329%), neg=0, invalid=96777

thanks for the comments.

Pom

-- Pom