Excellent! Thank you for the quick advice, I tried this initially but I was using the wrong xfm format.
Since I have the FA map in subject ?h.white space, I have done the same with the tract endings too. I am having some difficulties conceptually, in terms of projecting the end points onto either the subject specfic or fsaverage inflated surface. I assumed using mri_surf2surf would be sufficient to transform the endpts from subject surface ?h.white space to the inflated surface, but it is a scalar data file. Once the endpts are projected onto the inflated surface it seems straightforward to extract the thickness values for further analysis. Essentially replicating the attached image from Sølsnesa 2015. If you have any suggestions that would be much appreciated. Thank you very much! Best, Taha On Fri, Aug 19, 2016 at 9:49 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > 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 >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Taha Abdullah Department of Physiology Northwestern University Feinberg School of Medicine Masters of Science Physiology and Biophysics, Georgetown University 2015 Work: (312)-503-0413
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
