Below is the text of the process - it fails with no explanation. If anyone has any insight into this, it would be greatly appreciated!
[whatever:MYSTUDY] (nmr-std-env) tkregister-sess -sf sessid -df sesspar -------------------------------------------------------------- tkregister-sess logfile is /autofs/space/ship_006/users/kdevaney/Migraine_Aura/MYSTUDY/log/tkregister-sess.log --------------------------------------------------------------
Session: /autofs/space/ship_006/users/kdevaney/Migraine_Aura/analysis/Falco050630 ---------------- Mon Jan 2 19:41:16 EST 2006 INFO: anatdir set to /space/orsay/2/knutsen/falco/old/mri/T1 ________________________________________________ /autofs/space/ship_006/users/kdevaney/Migraine_Aura/analysis/Falco050630/bold/006 tkregister2 --targ /autofs/space/orsay_002/knutsen/falco/old/mri/T1 --mov ./f bshort --reg ../register.dat --plane cor --title old--Falco050630--006 --volview targ --surf white ________________________________________________ MRISread(/space/orsay/2/knutsen/falco/falco/surf/lh.white): could not open file No such file or directory tkregister2: could not read surface white No such file or directory surfname set to white target volume /autofs/space/orsay_002/knutsen/falco/old/mri/T1 movable volume ./f reg file ../register.dat LoadVol 1 $Id: tkregister2.c,v 1.30 2004/12/14 19:58:00 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- -0.348 0.013 0.005 -1.504; 0.014 0.325 0.078 20.196; 0.003 -0.073 0.337 10.458; 0.000 0.000 0.000 1.000; float2int = 0 --------------------------------------- INFO: loading target /autofs/space/orsay_002/knutsen/falco/old/mri/T1 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 ./f INFO: bvolumeRead: min = 0, max = 12970 INFO: changing move type to float Tmov: -------------------- -1.250 0.000 0.000 40.000; 0.000 0.000 1.250 -28.125; 0.000 -1.250 0.000 40.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -0.348 0.013 0.005 -1.504; 0.014 0.325 0.078 20.196; 0.003 -0.073 0.337 10.458; 0.000 0.000 0.000 1.000; subject = falco Reading lh surface white ERROR: tkregister2 failed [whatever:MYSTUDY] (nmr-std-env)
The error is actually burried in the output:
MRISread(/space/orsay/2/knutsen/falco/falco/surf/lh.white): could not open file No such file or directory
It looks like you moved falco to falco/old, which means that the subject name is "old" not "falco"
btw, I've changed tkregister-sess to bail out immediately if it cannot load the surface.
doug
Kathryn Devaney wrote:
Below is the text of the process - it fails with no explanation. If anyone has any insight into this, it would be greatly appreciated!
[whatever:MYSTUDY] (nmr-std-env) tkregister-sess -sf sessid -df sesspar
tkregister-sess logfile is /autofs/space/ship_006/users/kdevaney/Migraine_Aura/MYSTUDY/log/tkregister-sess.log
Session: /autofs/space/ship_006/users/kdevaney/Migraine_Aura/analysis/Falco050630
Mon Jan 2 19:41:16 EST 2006 INFO: anatdir set to /space/orsay/2/knutsen/falco/old/mri/T1 ________________________________________________ /autofs/space/ship_006/users/kdevaney/Migraine_Aura/analysis/Falco050630/bold/006 tkregister2 --targ /autofs/space/orsay_002/knutsen/falco/old/mri/T1 --mov ./f bshort --reg ../register.dat --plane cor --title old--Falco050630--006 --volview targ --surf white ________________________________________________ MRISread(/space/orsay/2/knutsen/falco/falco/surf/lh.white): could not open file No such file or directory tkregister2: could not read surface white No such file or directory surfname set to white target volume /autofs/space/orsay_002/knutsen/falco/old/mri/T1 movable volume ./f reg file ../register.dat LoadVol 1 $Id: tkregister2.c,v 1.30 2004/12/14 19:58:00 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- -0.348 0.013 0.005 -1.504; 0.014 0.325 0.078 20.196; 0.003 -0.073 0.337 10.458; 0.000 0.000 0.000 1.000; float2int = 0
INFO: loading target /autofs/space/orsay_002/knutsen/falco/old/mri/T1 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 ./f INFO: bvolumeRead: min = 0, max = 12970 INFO: changing move type to float Tmov: -------------------- -1.250 0.000 0.000 40.000; 0.000 0.000 1.250 -28.125; 0.000 -1.250 0.000 40.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -0.348 0.013 0.005 -1.504; 0.014 0.325 0.078 20.196; 0.003 -0.073 0.337 10.458; 0.000 0.000 0.000 1.000; subject = falco Reading lh surface white ERROR: tkregister2 failed [whatever:MYSTUDY] (nmr-std-env)
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Hi Kathryn,
it looks to me like the register.dat has the wrong subject name. There is no "falco" subject, rather a subject named "old" in the falco SUBJECTS_DIR:
ls /space/orsay/2/knutsen/falco/old/surf/ lh.area* lh.qsphere* rh.curv* rh.sphere* lh.curv* lh.rh.sphere.reg* rh.inflated* rh.sphere.reg* lh-dt_lop.label* lh.smoothwm* rh.orig* rh.sulc* lh.inflated* lh.sphere* rh.patch* rh.temporal.label* lh.MT* lh.sphere.reg* rh.patch.3d* rh.thickness* lh.orig* lh.sulc* rh.patch.flat* rh.white* lh.patch* lh-temporal.label* rh.pial* surfer.log* lh.patch.3d* lh.thickness* rh.qsphere* lh.patch.flat* lh.white* rh.rh.sphere.reg* lh.pial* rh.area* rh.smoothwm*
cheers, Bruce
On Mon, 2 Jan 2006, Kathryn Devaney wrote:
Below is the text of the process - it fails with no explanation. If anyone has any insight into this, it would be greatly appreciated!
[whatever:MYSTUDY] (nmr-std-env) tkregister-sess -sf sessid -df sesspar
tkregister-sess logfile is /autofs/space/ship_006/users/kdevaney/Migraine_Aura/MYSTUDY/log/tkregister-sess.log
Session: /autofs/space/ship_006/users/kdevaney/Migraine_Aura/analysis/Falco050630
Mon Jan 2 19:41:16 EST 2006 INFO: anatdir set to /space/orsay/2/knutsen/falco/old/mri/T1 ________________________________________________ /autofs/space/ship_006/users/kdevaney/Migraine_Aura/analysis/Falco050630/bold/006 tkregister2 --targ /autofs/space/orsay_002/knutsen/falco/old/mri/T1 --mov ./f bshort --reg ../register.dat --plane cor --title old--Falco050630--006 --volview targ --surf white ________________________________________________ MRISread(/space/orsay/2/knutsen/falco/falco/surf/lh.white): could not open file No such file or directory tkregister2: could not read surface white No such file or directory surfname set to white target volume /autofs/space/orsay_002/knutsen/falco/old/mri/T1 movable volume ./f reg file ../register.dat LoadVol 1 $Id: tkregister2.c,v 1.30 2004/12/14 19:58:00 greve Exp $ Diagnostic Level -1 ---- Input registration matrix -------- -0.348 0.013 0.005 -1.504; 0.014 0.325 0.078 20.196; 0.003 -0.073 0.337 10.458; 0.000 0.000 0.000 1.000; float2int = 0
INFO: loading target /autofs/space/orsay_002/knutsen/falco/old/mri/T1 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 ./f INFO: bvolumeRead: min = 0, max = 12970 INFO: changing move type to float Tmov: -------------------- -1.250 0.000 0.000 40.000; 0.000 0.000 1.250 -28.125; 0.000 -1.250 0.000 40.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- -0.348 0.013 0.005 -1.504; 0.014 0.325 0.078 20.196; 0.003 -0.073 0.337 10.458; 0.000 0.000 0.000 1.000; subject = falco Reading lh surface white ERROR: tkregister2 failed [whatever:MYSTUDY] (nmr-std-env)
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freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Doug Greve -
Kathryn Devaney