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 --------
-------------------------------------------
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
check the accuracy of the talairach transform by loading it in tkmedit and seeing if it looks reasonable. If it's not wrong, you'll need to specifiy seed points in mri_fill for the pons, callosum and/or the lh and rh white matter.
cheers, Bruce
On Fri, 29 Oct 2004, Wan Park wrote:
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 --------
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
You can also check (and fix!) the talairach registration with tkregister2. It's in the --help, but basically you just need to run:
tkregister2 --fstal --s subjectid
Don't re-run the talairaching or else you'll overwrite your manual registration.
doug
Bruce Fischl wrote:
check the accuracy of the talairach transform by loading it in tkmedit and seeing if it looks reasonable. If it's not wrong, you'll need to specifiy seed points in mri_fill for the pons, callosum and/or the lh and rh white matter.
cheers, Bruce
On Fri, 29 Oct 2004, Wan Park wrote:
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 --------
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
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Doug Greve -
Wan Park