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 <fis...@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 <
>> matthieuvanhou...@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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