Hello All,

I am trying to project FA map (dtifit_FA.nii.gz) and the endpt[1/2].pd.nii.gz from TRACULA onto fsaverage surface space. I was following instructions on http://web.mit.edu/fsl_v5.0.8/fsl/doc/wiki/FDT(2f)UserGuide.html, under FreeSurfer Registration, to create the various xfms files. 

Next, I registered the FA map to subject conformed space using flirt 
  • flirt -in dtifit_FA.nii.gz -ref ../../mri/orig.nii.gz -applyxfm -init ./xfms_taha/fa2freesurfer.mat -out fa2FS.nii.gz
Then, I used mri_vol2surf to project the registered FA map onto fsaverage surface with the following command. 
Upon viewing in freeview the fsavg rh.white surface and fa2FS.nii.gz (FA map in FreeSurfer space) did not allign properly. I have tried some variations wtihout any luck. I used the following command line for freeview.  
  • freeview -f /usr/local/freesurfer/subjects/fsaverage/surf/rh.white:overlay=FA_2fsavg_surf.mgh -v fa2FS.nii.gz
  • Attached are some pics of the FA confomred map and fsaverage.rh.white surface
Do I need a xfm file for taliarch allignment? Any advice or insight would be greatly appreciated.

Thanks in advance,
Taha 

Terminal output: from mri_vol2surf
srcvol = fa2FS.nii.gz
srcreg = ./xfms_taha/fa2freesurfer.mat
srcregold = 0
srcwarp unspecified
surf = white
hemi = rh
trgsubject = fsaverage
surfreg = sphere.reg
ProjDist = 0.5
reshape = 0
interp = nearest
float2int = round
GetProjMax = 1
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /usr/local/freesurfer/subjects/taha_brain/mri/orig.mgz as target reference.
Loading label /usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.label
Reading surface /usr/local/freesurfer/subjects/taha_brain/surf/rh.white
Done reading source surface
Mapping Source Volume onto Source Subject Surface
 1 6 6 6
using old
Done mapping volume to surface
Number of source voxels hit = 81606
Reading source surface registration 
  /usr/local/freesurfer/subjects/taha_brain/surf/rh.sphere.reg
Done loading source registration surface
Reading target registration 
   /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg
Done loading target registration surface
Mapping Surfaces (taha_brain -> fsaverage)
surf2surf_nnfr: building source hash (res=16).
Surf2Surf: Forward Loop (163842)

surf2surf_nnfr: building target hash (res=16).
Surf2Surf: Reverse Loop (143161)
Reverse Loop had 26084 hits
Surf2Surf: Dividing by number of hits (163842)
INFO: nSrcLost = 0
Done mapping surfaces
nSrc121 = 107182, nSrcLost =     0, nSrcMulti = 35979, MnSrcMultiHits = 2.29979
nTrg121 = 142955, nTrgMulti = 20887, MnTrgMultiHits = 2.24882
Masking with /usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.label
Writing to FA_2fsavg_surf.mgh
Dim: 163842 1 1


--
Taha Abdullah 
Department of Physiology
Northwestern University Feinberg School of Medicine 
Masters of Science Physiology and Biophysics, Georgetown University 2015
Work: (312)-503-0413