Dear freesurfers, I am trying to create .mgh labels in order to obtain CT averages from several subjects.
I register the ROI-s with bbregister and I get the .nii which renders nicely in tksurfer: tksurfer Surfrend_Colin127 lh inflated -overlay /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii -overlay-reg /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat -fthresh 1
The problem arises when I try to use mri_vol2surf. I've been trying with many different options, for example:
mri_vol2surf --mov /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii --reg /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat --projfrac 0.5 --projfrac-max 0 1 .01 --hemi lh --out /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh
or
mri_vol2surf --mov /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii --reg /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat --projdist-max 0 1 0.1 --projfrac 1 --interp nearest --hemi lh --out /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh
When I try to visualize it with tksurfer, it gives me nothing: tksurfer Surfrend_Colin27 lh inflated -label /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh -fthresh 1
How should I use mri_vol2surf in order to obtain results? What are the alternatives in order to have surface labels? Creating a label tracing the border of the .nii label in tksurfer is a posible solution?
Thank you very much for your attention, Gari
[iMacGari:~] garikoitz% mri_vol2surf --mov /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii --reg /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat --projfrac 0.5 --projfrac-max 0 1 .01 --hemi lh --out /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh srcvol = /Applications/freesurfer/subjects/ROI10/BrocaOrb_2mm.nii srcreg = /Applications/freesurfer/subjects/ROI10/bbregister_singlesubject_to_Colin.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 Done loading volume Reading surface /Applications/freesurfer/subjects/Surfrend_Colin127/surf/lh.white Done reading source surface Reading thickness /Applications/freesurfer/subjects/Surfrend_Colin127/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0 0 1 using old 2 0.01 0 1 using old 3 0.02 0 1 [...] 99 0.979999 0 1 using old 100 0.989999 0 1 using old 101 0.999999 0 1 using old Done mapping volume to surface Number of source voxels hit = 32875 Writing to /Applications/freesurfer/subjects/ROI10/lh.BA44-45-47.mgh Dim: 165607 1 1