did it have the correct orientation? Can you explain what the initial images were? Usually if you start from dicoms right from the scanner with a reasonable scan this isn't a problem so if it's happening frequently then it may be that something else is wrong.
cheers
Bruce
On Fri, 11 Dec 2015, Matthieu Vanhoutte wrote:
Hi Bruce,
Do you have an idea of what to do concerning this problem (below) ? I have
re-run with -notal-check and it worked not for all cases
Best regards,
Matthieu
2015-12-09 15:15 GMT+01:00 Matthieu Vanhoutte <matthieuvanhoutte@gmail.com>:
Hi Bruce,
I tried to follow the tutorial :
http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview
But nothing appeared in the image window of tkregister2 command...
Below you'll find the log of the command :
tkregister2 --mgz --s M0_2010-03-25 --fstal
tkregister_tcl /home/global//freesurfer5.3//tktools/tkregister2.tcl
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 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
%Fri Dec 4 15:13:39 2015>>>
/home/global//freesurfer5.3//mni/bin/minctracc -clobber -debug
/tmp/1504527.1.M32_q/mritotal_31071/src_8_dxyz.mnc/home/global//freesurfer5.3//mni/bin/../share/mni_autoreg/average_305_8_dxy
z.mnc transforms/talairach.auto.xfm -transformation
/tmp/1504527.1.M32_q/mritotal_31071/src_8tmp2c.xfm -lsq9 -xcorr
-model_mask/home/global//freesurfer5.3//mni/bin/../share/mni_autoreg/average_305_8_mas
k.mnc -center 5.299993 17.591406 -32.821045 -step 4 4 4 -tol 0.004
-simplex 2
talairach.xfm ---------------------
0.708 0.183 -0.254 -31.077;
-0.311 0.477 -0.525 -62.791;
0.033 0.582 0.509 156.288;
0.000 0.000 0.000 1.000;
INFO: loading target
/NAS/tupac/matthieu/FS5.3/M0_2010-03-25/mri/orig.mgz
Zeroing CRAS of target
new xfm -----------------
0.708 0.183 -0.254 -25.242;
-0.311 0.477 -0.525 -57.556;
0.033 0.582 0.509 165.535;
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/global//freesurfer5.3//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 --------
0.708 0.183 -0.254 -25.242;
-0.311 0.477 -0.525 -57.556;
0.033 0.582 0.509 165.535;
0.000 0.000 0.000 1.000;
Determinant 0.464133
subject = M0_2010-03-25
Zoom Factor = 2, SQR() = 4
FOV = 256
Opening window M0_2010-03-25
Opening M0_2010-03-25, xnum = 256, xdim = 512
Setting scale
tkregister2: interface:
/home/global//freesurfer5.3//tktools/tkregister2.tcl
tkregister.tcl: startup done
tkregister.tcl: default macro interface (to change: macro,mini,micro)
tkregister.tcl: or: setenv tkregisterinterface {macro,mini,micro}
T1.mgz, brainmask.mgz and subject's surfaces haven't been created yet.
I have checked that my input volume has the correct direction cosines.
Could you explain me what's wrong ?
Thanks !
Best regards,
Matthieu
2015-12-08 22:08 GMT+01:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>:
Hi Matthieu
did you check the talairach registration as suggested?
ALso, make sure that your input volume has the correct
direction cosines (that is, that what freeview thinks is
anterior is actually anterior, etc...)
cheers
Bruce
On Tue, 8 Dec 2015, Matthieu Vanhoutte wrote:
Dear FS experts,
I got no answer to my question. Could anyone
explain me what is the problem and how to
solve it ?
Best regards,
Matthieu
2015-12-04 16:11 GMT+01:00 Matthieu Vanhoutte
<matthieuvanhoutte@gmail.com>:
Dear experts,
I am confronted with some problem in the
"recon-all" of a few subjects concerning
Talairach
space, but don't know how to manage these.
Please find below the recon-all log with
errors :
#--------------------------------------------
#@# Talairach Failure Detection Fri Dec 4
15:29:38 CET 2015
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
talairach_afd -T 0.005 -xfm
transforms/talairach.xfm
talairach_afd: Talairach Transform:
transforms/talairach.xfm OK (p=0.6911,
pval=0.4932 >=
threshold=0.0050)
awk -f
/home/global//freesurfer5.3//bin/extract_talairach_avi_QA.awk
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri/transforms/talairach_avi.log
tal_QC_AZS
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri/transforms/talairach_avi.log
TalAviQA: 0.93027
z-score: -10
ERROR: Talairach QA check failed!
z-score = -10 <= -9 = threshold
atlas xform error = 0 < -60 | > 24
Manual Talairach alignment may be necessary,
or
include the -notal-check flag to skip this
test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
INFO: Attempting MINC mritotal to perform
Talairach align
#--------------------------------------------
#@# Talairach Fri Dec 4 15:29:39 CET 2015
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
mri_nu_correct.mni --n 1 --proto-iters 1000
--distance 50 --no-rescale --i orig.mgz --o
orig_nu.mgz
talairach --i orig_nu.mgz --xfm
transforms/talairach.auto.xfm
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
/home/global//freesurfer5.3//bin/talairach
--i orig_nu.mgz --xfm
transforms/talairach.auto.xfm
$Id: talairach,v 1.7 2011/03/02 20:16:40 nicks
Exp $
Linux wutang 3.13.0-24-generic #47-Ubuntu SMP
Fri May 2 23:30:00 UTC 2014 x86_64 x86_64
x86_64 GNU/Linux
Fri Dec 4 15:31:35 CET 2015
tmpdir is transforms/tmp.talairach.13347
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
mri_convert orig_nu.mgz
transforms/tmp.talairach.13347/src.mnc
mri_convert orig_nu.mgz
transforms/tmp.talairach.13347/src.mnc
$Id: mri_convert.c,v 1.179.2.7 2012/09/05
21:55:16 mreuter Exp $
reading from orig_nu.mgz...
TR=9.90, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (7.45058e-09, 1, 0)
writing to
transforms/tmp.talairach.13347/src.mnc...
--------------------------------------------
mritotal -verbose -debug -clobber -modeldir
/home/global//freesurfer5.3//mni/bin/../share/mni_autoreg
-protocol icbm
transforms/tmp.talairach.13347/src.mnc
transforms/talairach.auto.xfm
Fri Dec 4 15:31:58 CET 2015
talairach done
cp transforms/talairach.auto.xfm
transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Fri Dec 4
15:31:59 CET 2015
/NAS/tupac/matthieu/FS5.3/M0_2011-02-23/mri
talairach_afd -T 0.005 -xfm
transforms/talairach.xfm
ERROR: talairach_afd: Talairach Transform:
transforms/talairach.xfm ***FAILED***
(p=0.0039,
pval=0.0000 < threshold=0.0050)
Manual Talairach alignment may be necessary,
or
include the -notal-check flag to skip this
test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
See
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach
Linux wutang 3.13.0-24-generic #47-Ubuntu SMP
Fri May 2 23:30:00 UTC 2014 x86_64 x86_64
x86_64 GNU/Linux
recon-all -s M0_2011-02-23 exited with ERRORS
at Fri Dec 4 15:32:00 CET 2015
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Thanks in advance for helping !
Best regards,
Matthieu
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