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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