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
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