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

 

Sincerely yours,

 

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

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