Re: [Freesurfer] surf2vol ERROR
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 = 1.00 >> ysize = 1.00 >> zsize = 1.00 >> cdc = -1.00 0.00 -0.00 >> rdc = 0.00 -0.00 -1.00 >> sdc = 0.00 1.00 -0.00 >> 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 >> on behalf of >> Bruce Fischl >> 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 >> r
Re: [Freesurfer] surf2vol ERROR
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 on behalf of Bruce Fischl 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 > on behalf of > Bruce Fischl > 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 > > on behalf of > Bruce > > Fischl > > 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 > 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
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 on behalf of Bruce Fischl 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 on behalf of Bruce > Fischl > 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 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 on behalf of Bruce > > Fischl > > 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: &
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 on behalf of Bruce Fischl 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 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 on behalf of Bruce > Fischl > 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
Re: [Freesurfer] surf2vol ERROR
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<https://aka.ms/ghei36> From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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 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 > on behalf of Bruce > Fischl > 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
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 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 on behalf of Bruce Fischl 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
Re: [Freesurfer] surf2vol ERROR
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<https://aka.ms/ghei36> From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl 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
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] surf2vol ERROR
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
