Pedro Paulo,
Hi! Sita noticed that the file has a FOV > 256. We have found this to be a problem in processing, so beginning in v4.2.0, we exit with an error if it detects this. Normally he solution is simply to include the flag -cw256 on the recon-all command line. This crops the image to a FOV=256, and works in nearly all cases, but sometimes it crops into the brain, in which case some manual crop work may be necessary.
However, in the case of the file which you uploaded, the 001.mgz file looks unusual. The brain looks stretched in the S-I (z) direction, which I would expect would interfere with trying to align to the atlas during the skull-strip stage, which is likely why it failed. Do the original dicoms look the same?
Nick
On Thu, 2009-03-26 at 16:28 -0300, Pedro Paulo de Magalhães Oliveira Junior wrote:
There is a researcher here who is getting this error in version 4.2.0, I have uploaded the 001.mgz to the ftp:
****************TEMPLATE DEFORMATION****************
second estimation of the COG coord: x=150,y=117, z=145, r=8362iterations GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1073730580 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=20 , nb = -1073752625 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1073753196 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=26 , nb = -1601994905 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = -1073752746 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1768967209 mri_watershed Error: GLOBAL region of the brain empty ! Darwin lim44-macpro.local 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386
Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.netfilter.com.br
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer