It is possible but not easy. You'll have to start almost from scratch. Motion correct your time series. Then run mri_vol2surf to sample the time series on the surface (use nifti output). Smooth on the surface. Run FEAT using this as the input. Turn off spatial smoothing and prewhitening and masking (and anything else that might assume a volume structure). Tell it to save the residual error (can't remember how to do this). When you get that far, write back.
doug On 08/14/2014 09:31 AM, Milde, Christopher wrote: > > Dear Doug, > > thanks for your helpful comments according to the reading out fMRI > cluster peak vertices! > > Actually, I'm able now to read out cluster peak vertices (see bottom). > I applied the mri_surfcluster command for resampled and surface > smoothed Feat stats on smoothwm surface with projfrac 0.5 > (mri_surf2surf -fwhm). > > But I'm not sure how to apply Multiple Comparison Correction because I > only found this option for group statistics (mri_glmfit-sim). For this > purpose, I have to generate a GLM within Freesurfer. > > I use *FEAT preprocessed but unsmoothed data* and > coregistered/resampled it to the surfaces. My goal is to read out peak > vertices *on session/single-subject level*, preferentially on the > smoothwm with -projfrac 0.5. > > Is it possible to use the > mkanalysis-sess/mkcontrast-sess/selxvavg3-sess commands (seemingly > it’s just for FSFAST preprocessed data) in combination with a Multiple > Comparisons Correction at session level? OR Shall I run the > Preprocessing in FSFAST too? > > Hopefully, there is a solution for this delicate problem > > Sincerelyyours, > > Chris > > > mri_surfcluster --subject PM_00880_inflation --surf smoothwm --hemi lh > --in PM_00880_inflation/TR.feat/stats/smooth_10.mgz --thmin 2 --thmax > inf --sign pos --minarea 30 --annot aparc --sum > PM_00880_inflation/TR.feat/stats/TR_summary2 > thsign = pos, id = 1 > version $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ > hemi = lh > srcid = PM_00880_inflation/TR.feat/stats/smooth_10.mgz > srcsubjid = PM_00880_inflation > srcsurf = smoothwm > srcframe = 0 > thsign = pos > thmin = 2 > thmax = inf > fdr = -1 > minarea = 30 > xfmfile = talairach.xfm > nth = -1 > sumfile = PM_00880_inflation/TR.feat/stats/TR_summary2 > subjectsdir = /home/christopher/Desktop/freesurfer/subjects > FixMNI = 1 > ------------- XFM matrix (RAS2RAS) --------------- > /home/christopher/Desktop/freesurfer/subjects/PM_00880_inflation/mri/transforms/talairach.xfm > 1.052 0.044 -0.055 0.749; > -0.027 1.026 0.319 -8.121; > 0.030 -0.345 1.096 -13.593; > 0.000 0.000 0.000 1.000; > ---------------------------------------------------- > Reading source surface > /home/christopher/Desktop/freesurfer/subjects/PM_00880_inflation/surf/lh.smoothwm > Done reading source surface > Reading annotation > /home/christopher/Desktop/freesurfer/subjects/PM_00880_inflation/label/lh.aparc.annot > reading colortable from annotation file... > colortable with 36 entries read (originally > /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) > Computing metric properties > Loading source values > number of voxels in search space = 133455 > Done loading source values (nvtxs = 133455) > overall max = 5.55723 at vertex 63001 > overall min = -4.84855 at vertex 19315 > surface nvertices 133455 > surface area 79513.531250 > surface area 79513.859375 > Adjusting threshold for 1-tailed test. > If the input is not a -log10(p) volume, re-run with --no-adjust. > Searching for Clusters ... > thmin=2.000000 (1.698970), thmax=inf (inf), thsignid=1, minarea=30.000000 > Found 9 clusters > Max cluster size 1315.766113 > INFO: fixing MNI talairach coordinates > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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.
