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
#--------------------------------------------
[EMAIL PROTECTED] 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:
[EMAIL PROTECTED]:~/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
% [EMAIL PROTECTED]:~/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 ($session) set to:
surfer: /home/gacocco/freesurfer/subjects
surfer: Reading header info from
/home/gacocco/freesurfer/subjects/control_dr/mri/T1.mgz
surfer: vertices=108452, faces=216900
Loading /home/gacocco/freesurfer/surface_labels.txt
surfer: ### redraw failed: no gl window open
surfer: single buffered window
surfer: tkoInitWindow(control_dr)
surfer: using interface /home/gacocco/freesurfer/lib/tcl/tksurfer.tcl
Reading /home/gacocco/freesurfer/lib/tcl/tkm_common.tcl
Reading /home/gacocco/freesurfer/lib/tcl/tkm_wrappers.tcl
Reading /home/gacocco/freesurfer/lib/tcl/fsgdfPlot.tcl
Reading /home/gacocco/freesurfer/lib/tcl/tkUtils.tcl
Successfully parsed tksurfer.tcl
reading white matter vertex locations...
% [EMAIL PROTECTED]:~/freesurfer/subjects$ 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).
[EMAIL PROTECTED]:~/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
[EMAIL PROTECTED]:~/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
[EMAIL PROTECTED]:~/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
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