Great! looks good, thanks for the help. Enjoy your weekend!
On Fri, Aug 19, 2016 at 11:34 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Taha - Once you've mapped from the volume onto the white surface, you > should be able to display it on the inflated surface, and also to get > thickness statistics (thickness is just the distance between corresponding > points on the white and pial surface). You don't need to do anything to map > from white to inflated within an individual. > > Best, > a.y > > > On Fri, 19 Aug 2016, Taha Abdullah wrote: > > 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/subjec >> ts/fsaverage/surf/rh.white:overlay=FA_2fsavg_surf.m >> gh -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. > > -- 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.
