Hi Gari, those look correct (make sure that your indices are not off by 1 (ie, FS uses 0-based indexing, and matlab uses 1-based). I would not expect them to be the same since #1 includes a non-linear transform, and they are only off by about 1.5cm (not bad by affine standards). Not sure that one is better than the other, but #2 is probably more like what is in the liturature.
On 11/16/2016 04:53 PM, Garikoitz Lerma-Usabiaga wrote: > Hi all, > I have fMRI data in individual space, converted to individual surface > using vol2surf and to fsaverage surface using surf2surf (commands [1] > and [2] below). With Matlab, I obtain the vertex with the maximum > value: max_Vtx and max_Vtx305. If I would like to obtain the MNI152 > coordinate of this vertex (for comparison with the literature), I > think I have two options: > > 1.- Work in the individual space: > >> max_SurfaceRAS = lhwhite(max_Vtx, :); > >> max_RAS = T1.vox2ras*inv(T1.tkrvox2ras)*[max_SurfaceRAS';1]; > I can check in freeview that the result is correct. > >> max_RAS305 = TalXFM * max_RAS; > I can check in tkmedit that this is right too. > At last, using the MNI305to152 matrix provided by Doug in the wiki: > >> max_RAS152 = MNI305to152 * max_RAS305; > > 2.- Work in the fsaverage (305) space > >> max_SurfaceRAS305 = lhwhite305(max_Vtx305, :); > as Surface RAS is the same as RAS, we only have to convert it to 152 > >> max_RAS152_305 = MNI305to152 * max_SurfaceRAS305 ; > > The results are: > For 1: [-15.57, -93.62, -2.84] > For 2: [-23.06, -97.06, 1.35] > > Is this method ok? is this the way it should work? As the results are > not the same, is one of the methods inherently better than the other? > Many thanks! > Gari > > > [1] mri_vol2surf --srcsubject S001 --projfrac 0.5 --interp trilinear > --hemi lh --regheader S001 --mov fMRI.img --o fMRI.mgh > > [2] mri_surf2surf --srcsubject S001 --srchemi lh --srcsurfreg > sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg > --sval fMRI.mgh --tval fMRI305.mgh --sfmt curv --noreshape --no-cortex > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
