Hi Taha - Trying getting a .dat registration file from bbregister and using that as the input to mri_vol2surf. There's a multimodal tutorial on the freesurfer wiki that might be of help.
Best, a.y
On Thu, 18 Aug 2016, Taha Abdullah wrote:
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.
- mri_vol2surf --mov fa2FS.nii.gz --projdist-max 6 6 1 --cortex --hemi rh --trgsubject fsaverage --regheader taha_brain --reg ./xfms_taha/fa2freesurfer.mat --o FA_2fsavg_surf.mgh
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