The 27307 x 6 was originally done to be able to store data in nifti and analyze formats. They can be reshaped into a single vector of length 163842. When you load it into tksurfer, do you set the threshold to something very close to 0 to see if your values are just too small? Is everything 0 in matlab? Did you check the registration?
doug
Jing Ming wrote:
Hi Doug:
what I meant here is when we load output file on fsaverage surface, we can see nothing. And I have a question, why the mri_vol2surf need to reshape the whole vertex vector into 27307 x 6 dimention?
Reshaping 6 (nvertices = 163842)
Writing to ./sig-rh.mgh Dim: 27307 1 6
I have been able to load this mgh file into matlab, and should I just need to concatenate the six row of data to reconstruct a complete vector corresponding to the suface template?
Thanks much for your help!
Jing
Date: Mon, 13 Sep 2010 13:19:40 -0400 From: greve@nmr.mgh.harvard.edu To: mj_coming@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] problem of mri_vol2surf
what do you mean that you were not able to overlay it on the surface? What is actually going wrong? It looks like mri_vol2surf complete succesffully.
doug
Jing Ming wrote:
Hi surfers:
I was trying to convert a volume dataset from PET to fs surface template. The command I used is the following:
mri_vol2surf --src pet2t1.mgz --srcreg register.dat --hemi rh --o ./sig-rh.mgh --out_type mgh --float2int round --trgsubject ico --icoorder 7
The output file here is .mgh format. I also tried paint format. However, I was not able overlay the surface file (.mgh or .w) using freesufer. Is there anythign wrong with the command line?
Here is the the output log:
IcoOrder = 7, nIcoVtxs = 163842 srcvol = pet2t1.mgz srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = ico surfreg = sphere.reg interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Reading surface
/project/ADNI/PET/127_S_1210X1a_63646/127_S_1210X1a_63646/surf/rh.white
Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 vol2surf_linear: nhits = 152282/152282 Done mapping volume to surface Number of source voxels hit = 94326 Reading source surface registration
/project/ADNI/PET/127_S_1210X1a_63646/127_S_1210X1a_63646/surf/rh.sphere.reg
Done loading source registration surface Reading icosahedron, order = 7, radius = 100 Reading icosahedron /pkg/brainmap/freesurfer/lib/bem/ic7.tri Done loading target registration surface Mapping Surfaces (127_S_1210X1a_63646 -> ico) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842)
surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (152282) Reverse Loop had 34160 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 116454, nSrcLost = 0, nSrcMulti = 35828, MnSrcMultiHits
= 2.2761
nTrg121 = 138122, nTrgMulti = 25720, MnTrgMultiHits = 2.32815 Reshaping 6 (nvertices = 163842) Writing to ./sig-rh.mgh Dim: 27307 1 6
Thanks Jing Ming Northwestern University
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