Douglas,
The previous message had an images attached that seemed to be too big. it was "bounced" automatically. I guess too many images were attached.
I ran the command for the rh.white and lh.white and the image is not perfectly registered. I tried a lot of things, but nothing worked. I ended up using the idea from Bruce. I Binarized the aseg+aparc file, extracting the wm regions, eroded, and subtracted. That gave me a surface as a volumen. This also can be done with only the images (no need to extract the whole freesurfer output) The image from mri_surf2vol had better quality, but I couldn't get it to register. If by any chance someone figures this registration problem out, I will use certainly use it.
Thanks for all your help.
Gabriel
previous message:
Douglas,
I extracted the whole directory and ran:
mri_surf2vol --mkmask --surf white --hemi rh --o rh.white.mgz --template ../subjects/subject/mri/T1.mgz --sd ../subjects --subject subject --identity subject gdiagno = -1 Using identity matrix for registration Overriding reg subject subject with subject 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 ../subjects hemi rh mksurfmask 1 projfrac 0 outvol path rh.white.mgz template path ../subjects/subject/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 = 3.373505 20.515587 -6.721008 Gdiag_no -1 Reading surface ../subjects/subject/surf/rh.white Done reading source surface surf nframes = 1 INFO: mapping vertices to closest voxel INFO: resampling surface to volume INFO: sampled 84160 voxels in the volume INFO: writing output volume to rh.white.mgz done
I did both hemispheres, they are not registered. I tried using as template the T1.mgz, and T1 converted to nifti. I also tried output as mgz and then mri_convert to nifti, the also output to nifti. I always obtained the same volumes, and they were always unregistered.
both hemispheres, they are not registered. I tried using as template the T1.mgz, and T1 converted to nifti. I also tried output as mgz and then mri_convert to nifti, the also output to nifti.
[image: Inline image 2]
