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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