Dear Doug, Thank you very much for your reply.
There is one other thing that is not clear to me. When displaying group level FSL zstats onto the FreeSurfer surface, which threshold (-log10(p) or z score) should I use? Is it again -log10(p), and therefore p=.01 is 2? If this is indeed the case, how come that the min and max values that appear in the min and max of the X axis Range (in the configure overlay display window) are the actual minimum and maximum values of the z stat map generated in FSL? This is why I thought that the value used for thresholding the maps should be a z score value, i.e. for p=0.01, I would have used min=2.3 (one-tailed). What am I missing? Thanks again! Nicole On Mar 26, 2012, at 4:23 PM, Douglas N Greve wrote: > > > Zurcher Nicole wrote: >> >> Hi everyone, >> I have two questions regarding FreeSurfer and FSL interoperation and it >> would be great if someone could help. >> >> 1) When displaying subject-level FSL FEAT data onto the FS volume using the >> command "tkmedit blobby orig.mgz lh.white -overlay >> ./featdir/stats/zstat1.nii.gz -overlay-reg >> featdir/reg/freesurfer/anat2exf.register.dat fthresh 1.3 -fmid 2.3 -fslope >> 1” (mentioned on http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html) What >> /p/-value does the threshold of 1.3 correspond to? Is it a zscore? > It is -log10(p), so p=.01 is 2 >> >> 2) What would be the best way to display FSL group-level FEAT data (zstats) >> onto the FreeSurfer surface? >> As far as I understand, the FSL and FreeSurfer Interoperation website >> explains how to display subject level-feat on the surface. For the >> group-level data, it only explains how to run group-level analyses using >> mri_glmfit based on lower-level FSL FEAT directories. Is there a way to >> directly map the zstats from FSL group-level analyses onto the FreeSurfer >> surface? > You can use the $FREESURFER_HOME/average/mni152.register.dat. Note that this > is for display only. You still have all the shortcomings of doing the > analysis in the volume. > doug >> >> Thanks in advance for the help! >> Nicole >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 > > > > 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. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
