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