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-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/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-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 >> > > > > >> > > > > >> > > > > >> > > > > >> > > > >> > > > >> > > >> > > >> > >> > >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
