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
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
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 Androidhttps://aka.ms/ghei36
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu 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
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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu 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
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 Androidhttps://aka.ms/ghei36
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu 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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu 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
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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu 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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu 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
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/surf2vol/MS089_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/surf2vol/MS089_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/surf2vol/MS089_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/surf2vol/MS089_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/surf2vol/MS089_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/surf2vol/MS089_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/surf2vol/MS089_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/surf2vol/MS089_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/surf2vol/MS089_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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu 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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu 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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu 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
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/surf2vol/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/surf2vol/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/surf2vol/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/surf2vol/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/surf2vol/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/surf2vol/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/surf2vol/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/surf2vol/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/surf2vol/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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu 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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of
Bruce
Fischl fischl@nmr.mgh.harvard.edu 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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf
of Bruce
Fischl fischl@nmr.mgh.harvard.edu 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
Ha ok I had read it on freewiki and it was --identify
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surf2vol
Looks like it's working now, thanks! Vale ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu 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/surf2vol/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/surf2vol/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/surf2vol/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/surf2vol/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/surf2vol/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/surf2vol/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/surf2vol/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/surf2vol/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/surf2vol/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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu 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"
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From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of
Bruce
Fischl fischl@nmr.mgh.harvard.edu 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.
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From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf
of Bruce
Fischl fischl@nmr.mgh.harvard.edu 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
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/MS089_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/MS089_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/MS089_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/MS089_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/MS089_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/MS089_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/MS089_R01_29/CME_MS089_R01_29.nii.gz
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu 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/surf2vol/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/surf2vol/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/surf2vol/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/surf2vol/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/surf2vol/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/surf2vol/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/surf2vol/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/surf2vol/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/surf2vol/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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu 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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of
Bruce
Fischl fischl@nmr.mgh.harvard.edu 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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf
of Bruce
Fischl fischl@nmr.mgh.harvard.edu 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
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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu 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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu 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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf
of
Bruce
Fischl fischl@nmr.mgh.harvard.edu 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.
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From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on
behalf
of Bruce
Fischl fischl@nmr.mgh.harvard.edu 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
yes, run it twice. The second time specify the output of the first run with --merge
On 2/17/19 3:29 PM, Bruce Fischl wrote:
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: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu 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: freesurfer-bounces@nmr.mgh.harvard.edu
freesurfer-bounces@nmr.mgh.harvard.edu on behalf of
Bruce Fischl fischl@nmr.mgh.harvard.edu 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"
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From: freesurfer-bounces@nmr.mgh.harvard.edu
freesurfer-bounces@nmr.mgh.harvard.edu on behalf of
Bruce
Fischl fischl@nmr.mgh.harvard.edu 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: freesurfer-bounces@nmr.mgh.harvard.edu
freesurfer-bounces@nmr.mgh.harvard.edu on behalf
of Bruce
Fischl fischl@nmr.mgh.harvard.edu 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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Barletta, Valeria -
Bruce Fischl -
Greve, Douglas N.,Ph.D.