mri_surfcluster will probably do what you need though there are some caveats: - You will not be able to get the results corrected for multiple comparisons - If you are looking at the z-score, then this will not be as powerful as it could be because you applied no smoothing (unless you applied volume smoothing, then you have the disadvantages of volume smoothing)
I can't help you out with your mri_surfclsuter command line unless you send it along with the terminal output
On 8/12/14 8:59 AM, Milde, Christopher wrote:
Dear Freesurfers,
I'm struggling with finding a way of getting a table of the cluster maxima of FEAT functional data registered to (reg-feat2anat) and resampled to (feat2surf) reconstructed surfaces. I want to extract cluster maxima for single subjects but preferentially NOT in fsaverage group space.
The command mri_surfcluster seems to be quite promising for this purpose. Specifically the summary file with the VtxMax
*But, seemingly I use the wrong input file (-in) for the FEAT functional data (Error wrong type for mghRead).
1.) Is it at all possible to read resampled Feat data with mri_surfcluster?
2.) is it a prerequisite to run mri_glmfit as suggested in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat (I do not want to perform analysis in group space)
I'm very thankful for advice
Sincerely yours,
Chris
$ mri_surfcluster --subject PM_02173_inflation --in PM_02173_inflation/ML_us.feat/stats/zstat1.mgh --hemi lh --surf smoothwm --thmin 2 --thmax inf --sign pos --minarea 15 --annot aparc
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_02173_inflation/ML_us.feat/stats/zstat1.mgh srcsubjid = PM_02173_inflation srcsurf = smoothwm srcframe = 0 thsign = pos thmin = 2 thmax = inf fdr = -1 minarea = 15 xfmfile = talairach.xfm nth = -1 subjectsdir = /home/christopher/Desktop/freesurfer/subjects FixMNI = 1 ------------- XFM matrix (RAS2RAS) --------------- /home/christopher/Desktop/freesurfer/subjects/PM_02173_inflation/mri/transforms/talairach.xfm 1.127 -0.010 -0.020 0.954; 0.005 0.993 0.048 -16.639; 0.017 -0.052 1.162 -15.969; 0.000 0.000 0.000 1.000;
Reading source surface /home/christopher/Desktop/freesurfer/subjects/PM_02173_inflation/surf/lh.smoothwm Done reading source surface Reading annotation /home/christopher/Desktop/freesurfer/subjects/PM_02173_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 mghRead(PM_02173_inflation/ML_us.feat/stats/zstat1.mgh, -1): could not open file ERROR: could not read PM_02173_inflation/ML_us.feat/stats/zstat1.mgh as type
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