Hi,
my name is giovanni, hope you can help me...
i started the command
recon-all -s patient_lyp -all
on a folder containing the data of one of my patients...
after few minutes I got this error message:
########################################################################### Thu Jun 5 08:13:09 BST 2008 talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#-------------------------------------------- #@# Talairach Failure Detection Thu Jun 5 08:13:10 BST 2008 /home/gacocco/freesurfer/subjects/patient_lyp/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5852, pval=0.2817 >= threshold=0.0050)
awk -f /home/gacocco/freesurfer/bin/extract_talairach_avi_QA.awk /home/gacocco/freesurfer/subjects/patient_lyp/mri/transforms/talairach_avi.log
TalAviQA: 0.95959 z-score: -4 ERROR: Talairach QA check failed! z-score = -4 <= -4 = threshold Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux pc244-174 2.6.24-17-generic #1 SMP Thu May 1 14:31:33 UTC 2008 i686 GNU/Linux
recon-all exited with ERRORS at Thu Jun 5 08:13:11 BST 2008
############################################################################
I went to the page indicated by the message
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
and followed the instructions... so I typed in the terminal:
gacocco@pc244-174:~/freesurfer/subjects$ tkmedit control_dr orig.mgz
and i got this message:
############################################################################ Reading /home/gacocco/freesurfer/lib/tcl/tkm_common.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/gacocco/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkUtils.tcl % gacocco@pc244-174:~/freesurfer/subjects$ tksurfer control_dr rh pial surfer: current subjects dir: /home/gacocco/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/gacocco/freesurfer/subjects surfer: Reading header info from /home/gacocco/freesurfer/subjects/control_dr/mri/T1.mgz surfer: vertices=108452, faces=216900 Loading /home/gacocco/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(control_dr) surfer: using interface /home/gacocco/freesurfer/lib/tcl/tksurfer.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_common.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/gacocco/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % gacocco@pc244-174:~/freesurfer/subjects$ tksurfer control_dr rh pial surfer: current subjects dir: /home/gacocco/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/gacocco/freesurfer/subjects surfer: Reading header info from /home/gacocco/freesurfer/subjects/control_dr/mri/T1.mgz surfer: vertices=108452, faces=216900 Loading /home/gacocco/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(control_dr) surfer: using interface /home/gacocco/freesurfer/lib/tcl/tksurfer.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_common.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/gacocco/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) Found embedded color table in annotation. surfer: dmin=12.2021, vno=73320, x=45.2575, y=-2.4731, z=41.6030 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 73320 marked (curv=0.000000, stat=0.000000) x = (45.3, -2.5, 41.6), n = (-0.3, 0.9, 0.4). surfer: dmin=0.3104, vno=76989, x=36.2031, y=1.3400, z=30.5769 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 76989 marked (curv=0.000000, stat=0.000000) x = (36.2, 1.3, 30.6), n = (0.7, 0.5, 0.5). surfer: dmin=0.4661, vno=76851, x=33.4849, y=1.2373, z=45.7916 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 76851 marked (curv=0.000000, stat=0.000000) x = (33.5, 1.2, 45.8), n = (0.3, 0.9, -0.4). surfer: dmin=0.2625, vno=71233, x=20.1145, y=-4.2706, z=67.2250 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 71233 marked (curv=0.000000, stat=0.000000) x = (20.1, -4.3, 67.2), n = (0.4, 0.9, -0.0). surfer: dmin=0.6131, vno=66208, x=37.6014, y=-9.3269, z=62.7725 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 66208 marked (curv=0.000000, stat=0.000000) x = (37.6, -9.3, 62.8), n = (0.9, 0.3, -0.3). surfer: dmin=0.6404, vno=70561, x=57.4662, y=-4.9873, z=31.2062 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 70561 marked (curv=0.000000, stat=0.000000) x = (57.5, -5.0, 31.2), n = (0.8, 0.4, 0.4). surfer: dmin=0.6560, vno=73265, x=44.8697, y=-2.3008, z=44.3611 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 73265 marked (curv=0.000000, stat=0.000000) x = (44.9, -2.3, 44.4), n = (0.1, 0.9, -0.4). gacocco@pc244-174:~/freesurfer/subjects$ tkmedit patient_lyp brainmask.mgz Reading /home/gacocco/freesurfer/lib/tcl/tkm_common.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/gacocco/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkUtils.tcl gacocco@pc244-174:~/freesurfer/subjects$ tkregister2 --mgz --s patient_lyp --fstal --surf origsurfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 ZeroCRAS 1 $Id: tkregister2.c,v 1.86.2.2 2008/03/10 14:02:35 nicks Exp $ Diagnostic Level -1
% tkregister2
talairach.xfm --------------------- 1.263 -0.018 -0.037 1.562; 0.062 1.083 0.453 4.335; 0.041 -0.467 1.180 20.571; 0.000 0.000 0.000 1.000; INFO: loading target /home/gacocco/freesurfer/subjects/patient_lyp/mri/orig.mgz Zeroing CRAS of target new xfm ----------------- 1.263 -0.018 -0.037 4.634; 0.062 1.083 0.453 5.415; 0.041 -0.467 1.180 -14.586; 0.000 0.000 0.000 1.000; --------------------- INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /home/gacocco/freesurfer/average/mni305.cor.mgz INFO: changing move type to float Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.263 -0.018 -0.037 4.634; 0.062 1.083 0.453 5.415; 0.041 -0.467 1.180 -14.586; 0.000 0.000 0.000 1.000; subject = patient_lyp Reading lh surface orig MRISread(/home/gacocco/freesurfer/subjects/patient_lyp/surf/lh.orig): could not open file No such file or directory tkregister2.bin: could not read surface orig No such file or directory gacocco@pc244-174:~/freesurfer/subjects$ ############################################################################
So I typed:
tkregister2 --mgz --s patient_lyp --fstal
This time the utility starts, according to waht it says in the tutorial, but i do not see the green lines that should help me to stretch, translate, and rotate my MOVEABLE volume.
Where am i wrong?
best regards
giovanni antonio cocco
Hi Giovonni,
it stopped after detecting an unlikely transform, so no surfaces were created. You could run
recon-all -s patient_lyp -all -notal-check
which will skip the checking of the talairach xform, but if it is really wrong then things may feel. You can still use tkregister2 to do the alignment manually, you'll just need to click the "compare" button to flip back and forth between the subject volume and the talairach one.
cheers, Bruce
On Wed, 11 Jun 2008 skgtgac@ucl.ac.uk wrote:
Hi,
my name is giovanni, hope you can help me...
i started the command
recon-all -s patient_lyp -all
on a folder containing the data of one of my patients...
after few minutes I got this error message:
########################################################################### Thu Jun 5 08:13:09 BST 2008 talairach_avi done
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#-------------------------------------------- #@# Talairach Failure Detection Thu Jun 5 08:13:10 BST 2008 /home/gacocco/freesurfer/subjects/patient_lyp/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5852, pval=0.2817 >= threshold=0.0050)
awk -f /home/gacocco/freesurfer/bin/extract_talairach_avi_QA.awk /home/gacocco/freesurfer/subjects/patient_lyp/mri/transforms/talairach_avi.log
TalAviQA: 0.95959 z-score: -4 ERROR: Talairach QA check failed! z-score = -4 <= -4 = threshold Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux pc244-174 2.6.24-17-generic #1 SMP Thu May 1 14:31:33 UTC 2008 i686 GNU/Linux
recon-all exited with ERRORS at Thu Jun 5 08:13:11 BST 2008
############################################################################
I went to the page indicated by the message
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
and followed the instructions... so I typed in the terminal:
gacocco@pc244-174:~/freesurfer/subjects$ tkmedit control_dr orig.mgz
and i got this message:
############################################################################ Reading /home/gacocco/freesurfer/lib/tcl/tkm_common.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/gacocco/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkUtils.tcl % gacocco@pc244-174:~/freesurfer/subjects$ tksurfer control_dr rh pial surfer: current subjects dir: /home/gacocco/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/gacocco/freesurfer/subjects surfer: Reading header info from /home/gacocco/freesurfer/subjects/control_dr/mri/T1.mgz surfer: vertices=108452, faces=216900 Loading /home/gacocco/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(control_dr) surfer: using interface /home/gacocco/freesurfer/lib/tcl/tksurfer.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_common.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/gacocco/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % gacocco@pc244-174:~/freesurfer/subjects$ tksurfer control_dr rh pial surfer: current subjects dir: /home/gacocco/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/gacocco/freesurfer/subjects surfer: Reading header info from /home/gacocco/freesurfer/subjects/control_dr/mri/T1.mgz surfer: vertices=108452, faces=216900 Loading /home/gacocco/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(control_dr) surfer: using interface /home/gacocco/freesurfer/lib/tcl/tksurfer.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_common.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/gacocco/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) Found embedded color table in annotation. surfer: dmin=12.2021, vno=73320, x=45.2575, y=-2.4731, z=41.6030 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 73320 marked (curv=0.000000, stat=0.000000) x = (45.3, -2.5, 41.6), n = (-0.3, 0.9, 0.4). surfer: dmin=0.3104, vno=76989, x=36.2031, y=1.3400, z=30.5769 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 76989 marked (curv=0.000000, stat=0.000000) x = (36.2, 1.3, 30.6), n = (0.7, 0.5, 0.5). surfer: dmin=0.4661, vno=76851, x=33.4849, y=1.2373, z=45.7916 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 76851 marked (curv=0.000000, stat=0.000000) x = (33.5, 1.2, 45.8), n = (0.3, 0.9, -0.4). surfer: dmin=0.2625, vno=71233, x=20.1145, y=-4.2706, z=67.2250 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 71233 marked (curv=0.000000, stat=0.000000) x = (20.1, -4.3, 67.2), n = (0.4, 0.9, -0.0). surfer: dmin=0.6131, vno=66208, x=37.6014, y=-9.3269, z=62.7725 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 66208 marked (curv=0.000000, stat=0.000000) x = (37.6, -9.3, 62.8), n = (0.9, 0.3, -0.3). surfer: dmin=0.6404, vno=70561, x=57.4662, y=-4.9873, z=31.2062 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 70561 marked (curv=0.000000, stat=0.000000) x = (57.5, -5.0, 31.2), n = (0.8, 0.4, 0.4). surfer: dmin=0.6560, vno=73265, x=44.8697, y=-2.3008, z=44.3611 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 73265 marked (curv=0.000000, stat=0.000000) x = (44.9, -2.3, 44.4), n = (0.1, 0.9, -0.4). gacocco@pc244-174:~/freesurfer/subjects$ tkmedit patient_lyp brainmask.mgz Reading /home/gacocco/freesurfer/lib/tcl/tkm_common.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/gacocco/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkUtils.tcl gacocco@pc244-174:~/freesurfer/subjects$ tkregister2 --mgz --s patient_lyp --fstal --surf origsurfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 ZeroCRAS 1 $Id: tkregister2.c,v 1.86.2.2 2008/03/10 14:02:35 nicks Exp $ Diagnostic Level -1
% tkregister2
talairach.xfm --------------------- 1.263 -0.018 -0.037 1.562; 0.062 1.083 0.453 4.335; 0.041 -0.467 1.180 20.571; 0.000 0.000 0.000 1.000; INFO: loading target /home/gacocco/freesurfer/subjects/patient_lyp/mri/orig.mgz Zeroing CRAS of target new xfm ----------------- 1.263 -0.018 -0.037 4.634; 0.062 1.083 0.453 5.415; 0.041 -0.467 1.180 -14.586; 0.000 0.000 0.000 1.000;
INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /home/gacocco/freesurfer/average/mni305.cor.mgz INFO: changing move type to float Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.263 -0.018 -0.037 4.634; 0.062 1.083 0.453 5.415; 0.041 -0.467 1.180 -14.586; 0.000 0.000 0.000 1.000; subject = patient_lyp Reading lh surface orig MRISread(/home/gacocco/freesurfer/subjects/patient_lyp/surf/lh.orig): could not open file No such file or directory tkregister2.bin: could not read surface orig No such file or directory gacocco@pc244-174:~/freesurfer/subjects$ ############################################################################
So I typed:
tkregister2 --mgz --s patient_lyp --fstal
This time the utility starts, according to waht it says in the tutorial, but i do not see the green lines that should help me to stretch, translate, and rotate my MOVEABLE volume.
Where am i wrong?
best regards
giovanni antonio cocco
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
skgtgac＠ucl.ac.uk