ERROR: Talairach QA check failed! and ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED***
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
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
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
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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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_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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Bruce,
How can I check if I have the correct orientation ? The initial image look as classical T1 weighted.
I have the problem only on one subject above all, so that sounds like an exception ?
Best regards,
Matthieu
2015-12-11 14:49 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
if it's only on one subject then it probably isn't an orientation problem. Checking it just means bringing it up in freeview and making sure that the directions that freeview shows (left/right, I/S, A/P) are actually the anatomical ones in the image.
Probably the orientation is right and the talairach just failed. There are instructions for checking and correcting the talairach.xfm on our wiki.
cheers Bruce
On Mon, 14 Dec 2015, Matthieu Vanhoutte wrote:
Hi Bruce,
How can I check if I have the correct orientation ? The initial image look as classical T1 weighted.
I have the problem only on one subject above all, so that sounds like an exception ?
Best regards,
Matthieu
2015-12-11 14:49 GMT+01:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: 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/averag e_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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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