Thanks Doug, this answers the question. I will use the fsaverage data for between subject comparison and literature comparison then. Thanks! Gari PS: yes, the +1 and the xy flipping thing are a real pita :)
On Fri, Nov 18, 2016 at 5:54 PM Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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. > >
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