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