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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer