That one now automatically does subcortical segmentation, which will
take about 24 hours. Add -nosubcortseg to the command-line (AFTER
-stage1) to disable it.
doug
Timothy O'Keefe wrote:
Also, I am using the OSX Tiger snapshot of FreeSurfer with a new
recon-all script courtesy of Doug Greve.
On Jul 18, 2005, at 10:03 AM, Timothy O'Keefe wrote:
I ran recon-all stage1 and it took a very long time. Well, at least
longer than people document. I didn't time it, but it must have
taken close to 10 hours.
Also I received this error during mri_fill():
...
using +/- offset search region where offset is 39.....
using +/- offset search region where offset is 42.....
using +/- offset search region where offset is 45.....
using +/- offset search region where offset is 48.....
mri_fill: could not find pons
No such file or directory
INFO: Modifying dst c_(r,a,s), using the transform dst
INFO: Modifying dst c_(r,a,s), using the transform dst
INFO: Modifying dst c_(r,a,s), using the transform dst
talairach cc position changed to (0.90, -7.51, 23.75)
INFO: Modifying dst c_(r,a,s), using the transform dst
INFO: Modifying dst c_(r,a,s), using the transform dst
find_cutting_plane:seed point not in structure! Searching
neighborhood...
find_cutting_plane:seed point not in structure! Searching
neighborhood...
ERROR: mri_fill exited with non-zero status
recon-all exited with errors at Sat Jul 16 01:13:52 EDT 2005
Are there any suggestions? I am using a single T1 (1x1x1) image
acquired from a Siemens 1.5T machine. I realize I should use
multiple images for averaging, however I am just trying to get a
feel for the software.
-T
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358
Fax: 617-726-7422
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