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_dxyz.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_mask.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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