when I run
recon-all -s uf1 -talairach (uf1 is the subject)
I receive this message:
$ ####################################### INFO: SUBJECTS_DIR is /Volumes/stem/freesurfer/subjects --------------------------------------------- Talairach Fri Oct 29 17:23:19 ADT 2004 /Volumes/stem/freesurfer/subjects/um1/mri talairach2 um1 INFO: registering um1 Fri Oct 29 17:23:19 ADT 2004 -------------------------------------------- mri_convert orig orig/orig.mnc mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -protocol icbm orig/orig.mnc transforms/talairach.xfm -------------------------------------------- mri_add_xform_to_header /Volumes/stem/freesurfer/subjects/um1/mri/transforms/talairach.xfm /Volumes/s m/freesurfer/subjects/um1/mri/orig /Volumes/stem/freesurfer/subjects/um1/mri/orig Fri Oct 29 17:25:26 ADT 2004 INFO: starting per-hemisphere operations ----- Starting Hemisphere rh -------- ----- Starting Hemisphere lh --------
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recon-all finished without error at Fri Oct 29 17:25:26 ADT 2004 done
but when I return to csurf and I try to create the surface, I receive this message when it is filling the white matter:
area[0] = 2 (min = 350, max = 790), aspect = 2.00 (min = 0.60, max = 1.20) need search nearby using +/- offset search region where offset is 3..... using +/- offset search region where offset is 6..... using +/- offset search region where offset is 9..... using +/- offset search region where offset is 12..... using +/- offset search region where offset is 15..... using +/- offset search region where offset is 18..... using +/- offset search region where offset is 21..... using +/- offset search region where offset is 24..... using +/- offset search region where offset is 27..... using +/- offset search region where offset is 30..... using +/- offset search region where offset is 33..... using +/- offset search region where offset is 36..... 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..... /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_fill: could not find pons No such file or directory INFO: volume does not have linear_transform set nor lta is given by option.-xform. INFO: use identity matrix as the talairach transform. INFO: use src volume parameters for the talairach volume. INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood... INFO: Modifying dst c_(r,a,s), using the transform dst talairach cc position changed to (2.00, 29.00, -8.00) INFO: Modifying dst c_(r,a,s), using the transform dst find_cutting_plane:seed point not in structure! Searching neighborhood...
Command Finished
Could you tell me what to do? Thanks
Wan