sorry, I'm not sure what your question is. You probably have to run it
twice - once for each hemi
cheers
Bruce
On Sun, 17 Feb 2019, Barletta, Valeria wrote:
It is actually registering only 1 hemi (screenshot), the last I type in the
command:
panarea:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3 $
mri_surf2vol
--subject MS089_R01_29 --hemi rh
--surfval/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
S089_R01_29/rh.MS089_R01_29.subjspace.mgh --merge
/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MS089_R01_29/mri/T1.mgz
--identity MS089_R01_29 --hemi lh
--surfval/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
S089_R01_29/lh.MS089_R01_29.subjspace.mgh --merge
/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MS089_R01_29/mri/T1.mgz
--identity MS089_R01_29
--o/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
S089_R01_29/CME_MS089_R01_29.nii.gz
gdiagno = -1
Using merge volume as template
Using identity matrix for registration
Overriding reg subject MS089_R01_29 with MS089_R01_29
Qa2v: SurfXYZ to VolCRS: ------------------------------
-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;
--------------------------------------------------
subjects dir
/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3
surface value path
/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
S089_R01_29/lh.MS089_R01_29.subjspace.mgh
hemi lh
mksurfmask 0
projfrac 0
outvol path
/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
S089_R01_29/CME_MS089_R01_29.nii.gz
template path
/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MS089_R01_29/mri/T1.mgz
------- Anat2Vol Registration (TkReg)----
1.000 0.000 0.000 0.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
-----------------------------------------
height = 256
width = 256
depth = 256
xsize = 1.000000
ysize = 1.000000
zsize = 1.000000
cdc = -1.000000 0.000000 -0.000000
rdc = 0.000000 -0.000000 -1.000000
sdc = 0.000000 1.000000 -0.000000
xyz0 = 3.587784 22.749557 -8.968880
Gdiag_no -1
Reading surface
/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MS089_R01_29/surf/lh.white
Done reading source surface
INFO: reading
/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
S089_R01_29/lh.MS089_R01_29.subjspace.mgh as MGH
Done loading source values (nvtxs = 137036)
INFO: mapping vertices to closest voxel
INFO: resampling surface to volume
INFO: sampled 85686 voxels in the volume
INFO: writing output volume
to/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vol/M
S089_R01_29/CME_MS089_R01_29.nii.gz
____________________________________________________________________________________________________
From: [email protected]
<[email protected]> on behalf of
Bruce Fischl <[email protected]>
Sent: Sunday, February 17, 2019 2:05:58 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] surf2vol ERROR
you have a typo. It's not "-identify" it is "--identity"
On Sun, 17 Feb
2019, Barletta, Valeria wrote:
>
> Sure... There is also a screenshot attached
>
>
> panarea:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3
$
> panarea:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3
$ mri_surf2vol
> --subject MS089_R01_29 --hemi
rh--surfval/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/s
urf2vol/M
> S089_R01_29/rh.MS089_R01_29.subjspace.mgh --hemi
lh--surfval/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/s
urf2vol/M
>
S089_R01_29/lh.MS089_R01_29.subjspace.mgh--o/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vo
l/M
> S089_R01_29/CME_MS089_R01_29.nii.gz --merge
>
/autofs/space/alicudi_002/users/mscat/users/celine/lesion_mask/MS089_R01_29/combined-CL.nii.gz
> --regheader MS089_R01_29
> ERROR: Option --regheader unknown
>
> panarea:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3
$ mri_surf2vol
> --subject MS089_R01_29 --hemi
rh--surfval/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/s
urf2vol/M
> S089_R01_29/rh.MS089_R01_29.subjspace.mgh --hemi
lh--surfval/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/s
urf2vol/M
>
S089_R01_29/lh.MS089_R01_29.subjspace.mgh--o/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vo
l/M
> S089_R01_29/CME_MS089_R01_29.nii.gz --merge
>
/autofs/space/alicudi_002/users/mscat/users/celine/lesion_mask/MS089_R01_29/combined-CL.nii.gz
> --trgsubject MS089_R01_29
> ERROR: Option --trgsubject unknown
>
> panarea:/autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3
$ mri_surf2vol
> --subject MS089_R01_29 --hemi
rh--surfval/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/s
urf2vol/M
> S089_R01_29/rh.MS089_R01_29.subjspace.mgh --hemi
lh--surfval/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/s
urf2vol/M
>
S089_R01_29/lh.MS089_R01_29.subjspace.mgh--o/autofs/space/alicudi_002/users/mscat/users/valeria/2017_CME_MTR_PET/2017_MTR_PET/GLM0.7/surf2vo
l/M
> S089_R01_29/CME_MS089_R01_29.nii.gz --merge
>
/autofs/space/alicudi_002/users/mscat/users/celine/lesion_mask/MS089_R01_29/combined-CL.nii.gz
> --identify MS089_R01_29
> ERROR: Option --identify unknown
>
>
>
>___________________________________________________________________________________________________
_
> From: [email protected]
<[email protected]> on behalf of
> Bruce Fischl <[email protected]>
> Sent: Sunday, February 17, 2019 11:08:41 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] surf2vol ERROR
> can you send us the full command line and screen output? You should not
> need a registration
>
> cheers
> Bruce
> On Sun, 17 Feb 2019, Barletta, Valeria wrote:
>
> > I need to turn my lh and rh .mgh files (they are in the subject's space) to
a single .nii.gz
file.
> Does
> > this process require a registration? I actually tried to use --identity
instead of --trgsubject,
> but I got
> > the same error, "Option --identity unknown"
> >
> >
> > Get Outlook for Android
> >
>>__________________________________________________________________________________________________
_
> _______
> > From: [email protected]
<[email protected]> on behalf
of
> Bruce
> > Fischl <[email protected]>
> > Sent: Sunday, February 17, 2019 10:56:33 AM
> > To: Freesurfer support list
> > Subject: Re: [Freesurfer] surf2vol ERROR
> > but do you need a registration? What space do you want the volume to be
> > in? If the standard FS "conformed" space you don't need a regisration (you
> > can specify --identity <subject ID). Or you can specify a registration
> > with --reg or --lta. In any case, mri_surf2vol has pretty good
> > documentation (thanks Doug!). Check out mri_surf2vol --help
> >
> > cheers
> > Bruce
> >
> >
> > On
> > Sun, 17 Feb 2019, Barletta, Valeria wrote:
> >
> > > Oh I just used that option instead of providing a registration file,
which I don't have.
> > > I need to turn the two surfaces into a single volume.
> > >
> > > Get Outlook for Android
> > >
>>>_________________________________________________________________________________________________
_
> _______
> > _
> > > From: [email protected]
<[email protected]> on
behalf
> of Bruce
> > > Fischl <[email protected]>
> > > Sent: Saturday, February 16, 2019 6:58:46 PM
> > > To: Freesurfer support list
> > > Subject: Re: [Freesurfer] surf2vol ERROR
> > > Hi Vale
> > >
> > > mri_surf2vol is to take take from the surface to the volume within one
> > > subject. Why do you need a trgsubject? You can compute the registration
> > > with e.g. bbregister. Maybe I'm not understanding what you are trying to
> > > do....
> > >
> > > cheers
> > > Bruce
> > >
> > > On Sat, 16 Feb 2019, Barletta, Valeria wrote:
> > >
> > > >
> > > > Dear all,
> > > >
> > > > I am trying to register surfaces to a volume by this command:
> > > >
> > > > mri_surf2vol --subject MS089_R01_29 --hemi rh
--rh.MS089_R01_29.subjspace.mgh --hemi lh
> --surfval
> > > > lh.MS089_R01_29.subjspace.mgh --o CME_MS089_R01_29.nii.gz --merge
combined-CL.nii.gz
--trgsubj
> > > > MS089_R01_29
> > > >
> > > >
> > > > And am obtaining this error:
> > > >
> > > > ERROR: Option --trgsubject unknown
> > > >
> > > >
> > > > That is actually the name of my subject in $FREESURFER_HOME
> > > >
> > > > Also, I do not have a registration file so I used the option
--trgsubject
> > > >
> > > > Is this correct? Why am I getting that error?
> > > >
> > > > Thanks,
> > > >
> > > > Vale
> > > >
> > > >
> > > >
> > > >
> > >
> > >
> >
> >
>
>
_______________________________________________
Freesurfer mailing list
[email protected]
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
