Hi,
I am trying to resample two volumetric data onto freesurfer individual subjects. The volume images are NIFTI format from SPM results (spmT_0001.img and con_0001.img). I used the following command to resample spmT map onto the surface:
mri_vol2surf --mov 3t0499/model/ravol/spmT_0001.img --reg
3t0499/register.dat --projfrac 0.5 --interp nearest --hemi lh --o ./lh.spmT_tmp.mgh --surf-fwhm 5 --noreshape > .mri_vol2surf.spmT.txt
and this worked fine when I checked lh.spmT_tmp.mgh using tksurfer. Similarly, I tried to resample the con_0001.img image, using the following command:
mri_vol2surf --mov 3t0499/model/ravol/con_0001.img --reg
3t0499/register.dat --projfrac 0.5 --interp nearest --hemi lh --o ./lh.con_tmp.mgh --surf-fwhm 5 --noreshape > .mri_vol2surf.con.txt
Now, when I checked the results using tksurfer, majority of the surface vertices are valued zero, and these zero-valued vertices were NaN's when I read the mgh file in matlab.
I expect the same resampling procedure to take place for the spmT map and the con map. There should be no difference between the spmT*.img and the con*.img except that the values at each voxel is different. But, why are the two *mgh files look so different? Why do I see NaN's in most of the vertices in the con*.mgh (while it seems spmT*.mgh looks fine)?
Joon
p.s. FYI, .mri_vol2surf.spmT.txt and mri_vol2surf.con.txt are below:
more .mri_vol2surf.spmT.txt
srcvol = 3t0499/model/ravol/spmT_0001.img srcreg = 3t0499/register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Reading surface ./3t0499/surf/lh.white Done reading source surface Reading thickness ./3t0499/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 Done mapping volume to surface Number of source voxels hit = 10273 Surface smoothing by fwhm = 5 (n=14) Smoothing done, nsteps = 14, tsec = 0.375 Writing to ./lh.spmT_tmp.mgh Dim: 144558 1 1
more .mri_vol2surf.con.txt
srcvol = 3t0499/model/ravol/con_0001.img srcreg = 3t0499/register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Reading surface ./3t0499/surf/lh.white Done reading source surface Reading thickness ./3t0499/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 Done mapping volume to surface Number of source voxels hit = 10273 Surface smoothing by fwhm = 5 (n=14) Smoothing done, nsteps = 14, tsec = 0.383 Writing to ./lh.con_tmp.mgh Dim: 144558 1 1