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-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@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-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of > Bruce Fischl <fis...@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-boun...@nmr.mgh.harvard.edu > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of > Bruce > > Fischl <fis...@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-boun...@nmr.mgh.harvard.edu > > > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf > of Bruce > > > Fischl <fis...@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 > > > > > > > > > > > > > > > > > > > > > > > > > > > >
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