The problem with doing the smoothing at the first level in FEAT is that it will be volume-based, not surface-based. I'm not sure what to tell you about using the varcopes. They will certainly be very noisy without smoothing, so probably smoothing is a good idea, even if it's volume-based.
doug Agnieszka Burzynska wrote: > Dear Doug, > Thank you so much. I completely see you point, but I have re-run the 1st > level feat without smoothing just because it has been recommended not to > smooth in the volume and then transfer it onto the surface, but rather first > smooth on the surface > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslFeatFreeSurfer). > > What I plan to do in the end is to include the cortical thickness as the > vertex-wise covariate in the functional group analysis. > > So the final analysis will be on the group level, where, as you say, the > varcopes should not matter that much. > > However, I was also thinking of analyzing varcopes in addition to copes > (group analysis) to relate the variance of BOLD signal to the thickness. > > Would you then recommend going back and taking the initial 1st level > analysis with regular smoothing? > > Thank you! > Aga > > On 7/7/11 4:43 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: > > >> Hi Aga, your commands look right. For the DOF, it should be the sum of >> the DOFs from all the runs (probably won't make much of a difference). >> Smoothing is a bit of an issue when you want to look at individual >> results. Technically, you should smooth before you do the first level >> analysis (ie, before your compute the varcope), but this would require >> doing the FEAT analysis directly on surface data. Smoothing after >> computing the varcope means that the varcope will not be accurate (it >> will be too large). The penalty is that you will see less activation >> than you should. At the group level, this is not such a big deal because >> you're either not using the varcope or you are using it as a weight. >> doug >> >> Agnieszka Burzynska wrote: >> >>> Dear all, >>> I am combining 3 runs of a subject using fixed effects GLM and I wanted to >>> make sure I am doing the right thing. >>> >>> For each subject I use: >>> mri_glmfit --y 3runs/lh.cope1.mgh --yffxvar 3runs/lh.varcope1.mgh --ffxdof >>> 126 --osgm --glmdir 3runs/lh.osgm.ffx --surf fsaverage lh --label >>> $SUBJECTS_DIR/fsaverage/label/lh.cortex.label --fwhm 5 >>> >>> , while lh.cope1.mgh contains the concatenated cope1 images of the same >>> subject in fsaverage space (the same for varcope1). >>> >>> 1) Is it the right way? >>> 2) I took DOF from subjectX.feat/stats/dof of one of the runs. Is it >>> correct? >>> 3) The functional data has not been smoothed in the 1st level analysis in >>> FSL (as recommended), and also not smoothed during sampling the copes to a >>> common space. Therefore I want to smooth it here for the first time, but >>> only with 5mm. Does it sound right? >>> >>> Cheers, >>> Aga >>> >>> _______________________________________________ >>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
