Hello Freesurfer experts,
After I run preproc-sess with this command ( preproc-sess -surface self lhrh -fwhm 5 -fsd Retinotopy -per-run -s Sess01 -s Sess02 ), I get an error saying that the register.dof6.dat file is missing and I should run register-sess to create it. When I run this with the debug option (register-sess -s Sess01 -s Sess02 -d . -fsd bold -per-run -debug) the system again fails to create the register file and gives pretty much the same error preproc-sess spit out:
MinCost: tkregister2_cmdl --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta regio_read_register(): No such file or directory Could not open bold/002/register.dof6.dat tkregister_tcl /home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/002/template.nii.gz reg file bold/002/register.dof6.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 ERROR: reading bold/002/register.dof6.dat Cleaning up
I thought of manually creating it with bbregister command but I am not sure about which scan I should use for "volume used for motion correction," and I would rather prefer to fix this with preproc-sess command.
Also I attached a portion from file "register.dof6.dat.log" file I could get for my each run. I hope these excerpts help. I would deeply appreciate any help.
Best, Idil
COREGpreproc() done Testing if mov and target overlap Numerical result out of range mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii --init-reg bold/002/tmp.bbregister.12926/reg.init.dat --out-reg bold/002/tmp.bbregister.12926/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open bold/002/tmp.bbregister.12926/reg.init.dat mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii --init-reg bold/002/tmp.bbregister.12926/bbr.pass1.dat --out-reg bold/002/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/002/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/002/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/002/tmp.bbregister.12926/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open bold/002/tmp.bbregister.12926/bbr.pass1.dat MinCost: tkregister2_cmdl --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta tkregister_tcl /home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/002/template.nii.gz reg file bold/002/register.dof6.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 ERROR: reading bold/002/register.dof6.dat Cleaning up
Started at Sun Oct 15 15:32:07 EDT 2017 Ended at Sun Oct 15 15:32:41 EDT 2017 BBR-Run-Time-Sec 34
bbregister Done To check results, run: tkregisterfv --mov bold/002/template.nii.gz --reg bold/002/register.dof6.lta --surfs
which version of FS are you using? Is this a new analysis done from scratch or had you preprocessed before?
On 10/15/17 4:10 PM, Yagmur Ozdemir 19 wrote:
Hello Freesurfer experts,
After I run preproc-sess with this command ( preproc-sess -surface self lhrh -fwhm 5 -fsd Retinotopy -per-run -s Sess01 -s Sess02 ), I get an error saying that the register.dof6.dat file is missing and I should run register-sess to create it. When I run this with the debug option (register-sess -s Sess01 -s Sess02 -d . -fsd bold -per-run -debug) the system again fails to create the register file and gives pretty much the same error preproc-sess spit out:
MinCost: tkregister2_cmdl --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta regio_read_register(): No such file or directory Could not open bold/002/register.dof6.dat tkregister_tcl /home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/002/template.nii.gz reg file bold/002/register.dof6.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 ERROR: reading bold/002/register.dof6.dat Cleaning up
I thought of manually creating it with bbregister command but I am not sure about which scan I should use for "volume used for motion correction," and I would rather prefer to fix this with preproc-sess command.
Also I attached a portion from file "register.dof6.dat.log" file I could get for my each run. I hope these excerpts help. I would deeply appreciate any help.
Best, Idil
COREGpreproc() done Testing if mov and target overlap Numerical result out of range mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii --init-reg bold/002/tmp.bbregister.12926/reg.init.dat --out-reg bold/002/tmp.bbregister.12926/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open bold/002/tmp.bbregister.12926/reg.init.dat mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii --init-reg bold/002/tmp.bbregister.12926/bbr.pass1.dat --out-reg bold/002/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/002/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/002/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/002/tmp.bbregister.12926/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open bold/002/tmp.bbregister.12926/bbr.pass1.dat MinCost: tkregister2_cmdl --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta tkregister_tcl /home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/002/template.nii.gz reg file bold/002/register.dof6.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 ERROR: reading bold/002/register.dof6.dat Cleaning up
Started at Sun Oct 15 15:32:07 EDT 2017 Ended at Sun Oct 15 15:32:41 EDT 2017 BBR-Run-Time-Sec 34
bbregister Done To check results, run: tkregisterfv --mov bold/002/template.nii.gz --reg bold/002/register.dof6.lta --surfs
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I am using version 6.0.0 and this is made from scratch. Just a couple of days ago I processed a different subject but used the special retinotopy procedure and didn't come across this problem. I first noticed this error in selxavg-sess and went back and used mkbrainmask, register-sess and preprocessed a couple of times again with -force and either per-run or -session to try troubleshooting.
Idil ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] Sent: Monday, October 16, 2017 6:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] register.dof6.dat file missing with register-sess
which version of FS are you using? Is this a new analysis done from scratch or had you preprocessed before?
On 10/15/17 4:10 PM, Yagmur Ozdemir 19 wrote: Hello Freesurfer experts,
After I run preproc-sess with this command ( preproc-sess -surface self lhrh -fwhm 5 -fsd Retinotopy -per-run -s Sess01 -s Sess02 ), I get an error saying that the register.dof6.dat file is missing and I should run register-sess to create it. When I run this with the debug option (register-sess -s Sess01 -s Sess02 -d . -fsd bold -per-run -debug) the system again fails to create the register file and gives pretty much the same error preproc-sess spit out:
MinCost: tkregister2_cmdl --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta regio_read_register(): No such file or directory Could not open bold/002/register.dof6.dat tkregister_tcl /home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/002/template.nii.gz reg file bold/002/register.dof6.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 ERROR: reading bold/002/register.dof6.dat Cleaning up
I thought of manually creating it with bbregister command but I am not sure about which scan I should use for "volume used for motion correction," and I would rather prefer to fix this with preproc-sess command.
Also I attached a portion from file "register.dof6.dat.log" file I could get for my each run. I hope these excerpts help. I would deeply appreciate any help.
Best, Idil
COREGpreproc() done Testing if mov and target overlap Numerical result out of range mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii --init-reg bold/002/tmp.bbregister.12926/reg.init.dat --out-reg bold/002/tmp.bbregister.12926/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open bold/002/tmp.bbregister.12926/reg.init.dat mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii --init-reg bold/002/tmp.bbregister.12926/bbr.pass1.dat --out-reg bold/002/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/002/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/002/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/002/tmp.bbregister.12926/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open bold/002/tmp.bbregister.12926/bbr.pass1.dat MinCost: tkregister2_cmdl --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta tkregister_tcl /home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/002/template.nii.gz reg file bold/002/register.dof6.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 ERROR: reading bold/002/register.dof6.dat Cleaning up
Started at Sun Oct 15 15:32:07 EDT 2017 Ended at Sun Oct 15 15:32:41 EDT 2017 BBR-Run-Time-Sec 34
bbregister Done To check results, run: tkregisterfv --mov bold/002/template.nii.gz --reg bold/002/register.dof6.lta --surfs
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I don't know what might be going wrong here. Have you tried to re-run it from scratch? Are you out of disk space?
On 10/16/17 12:59 PM, Yagmur Ozdemir 19 wrote:
I am using version 6.0.0 and this is made from scratch. Just a couple of days ago I processed a different subject but used the special retinotopy procedure and didn't come across this problem. I first noticed this error in selxavg-sess and went back and used mkbrainmask, register-sess and preprocessed a couple of times again with -force and either per-run or -session to try troubleshooting.
Idil
*From:* freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas Greve [greve@nmr.mgh.harvard.edu] *Sent:* Monday, October 16, 2017 6:18 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] register.dof6.dat file missing with register-sess
which version of FS are you using? Is this a new analysis done from scratch or had you preprocessed before?
On 10/15/17 4:10 PM, Yagmur Ozdemir 19 wrote:
Hello Freesurfer experts,
After I run preproc-sess with this command ( preproc-sess -surface self lhrh -fwhm 5 -fsd Retinotopy -per-run -s Sess01 -s Sess02 ), I get an error saying that the register.dof6.dat file is missing and I should run register-sess to create it. When I run this with the debug option (register-sess -s Sess01 -s Sess02 -d . -fsd bold -per-run -debug) the system again fails to create the register file and gives pretty much the same error preproc-sess spit out:
MinCost: tkregister2_cmdl --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta regio_read_register(): No such file or directory Could not open bold/002/register.dof6.dat tkregister_tcl /home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/002/template.nii.gz reg file bold/002/register.dof6.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 ERROR: reading bold/002/register.dof6.dat Cleaning up
I thought of manually creating it with bbregister command but I am not sure about which scan I should use for "volume used for motion correction," and I would rather prefer to fix this with preproc-sess command.
Also I attached a portion from file "register.dof6.dat.log" file I could get for my each run. I hope these excerpts help. I would deeply appreciate any help.
Best, Idil
COREGpreproc() done Testing if mov and target overlap Numerical result out of range mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii --init-reg bold/002/tmp.bbregister.12926/reg.init.dat --out-reg bold/002/tmp.bbregister.12926/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-frac 0.5 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open bold/002/tmp.bbregister.12926/reg.init.dat mri_segreg --mov bold/002/tmp.bbregister.12926/template.nii --init-reg bold/002/tmp.bbregister.12926/bbr.pass1.dat --out-reg bold/002/register.dof6.dat --interp trilinear --wm-proj-abs 2 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost bold/002/register.dof6.dat.mincost --dof 6 --nmax 36 --param bold/002/register.dof6.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg bold/002/tmp.bbregister.12926/reg.curopt.dat --gm-proj-frac 0.5 --nsub 1 --gm-gt-wm 0.5 regio_read_register(): No such file or directory Could not open bold/002/tmp.bbregister.12926/bbr.pass1.dat MinCost: tkregister2_cmdl --mov bold/002/template.nii.gz --reg bold/002/register.dof6.dat --noedit --ltaout bold/002/register.dof6.lta tkregister_tcl /home/cemnl-cmap/Desktop/freesurfer/tktools/tkregister2.tcl INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume bold/002/template.nii.gz reg file bold/002/register.dof6.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ Diagnostic Level -1 ERROR: reading bold/002/register.dof6.dat Cleaning up
Started at Sun Oct 15 15:32:07 EDT 2017 Ended at Sun Oct 15 15:32:41 EDT 2017 BBR-Run-Time-Sec 34
bbregister Done To check results, run: tkregisterfv --mov bold/002/template.nii.gz --reg bold/002/register.dof6.lta --surfs
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Yagmur Ozdemir 19