The command I used is mri_surfcluster --in sig.w --subject fsaverage --hemi lh
--annot aparc --sign pos --minarea 30 --sum area100.pos.cluster.summary --o
area100.pos.cluster.w --thmin 1.3
Teriminal output is
thsign = pos, id = 1
version $Id: mri_surfcluster.c,v 1.51.2.1 2011/03/28 15:32:36 greve Exp $
hemi = lh
srcid = sig.w
srcsubjid = fsaverage
srcsurf = white
srcframe = 0
thsign = pos
thmin = 1.3
thmax = -1
fdr = -1
minarea = 30
xfmfile = talairach.xfm
nth = -1
outid = area100.pos.cluster.w paint
sumfile = area100.pos.cluster.summary
subjectsdir = /isilon/work/FBIP/0_projects/freesurfer/subjects
FixMNI = 1
------------- XFM matrix (RAS2RAS) ---------------
/isilon/work/FBIP/0_projects/Pinna/freesurfer/subjects/fsaverage/mri/transforms/talairach.xfm
1.000 0.000 0.000 0.000;
0.000 1.000 0.000 0.000;
0.000 0.000 1.000 0.000;
0.000 0.000 0.000 1.000;
----------------------------------------------------
Reading source surface
/isilon/work/FBIP/0_projects/freesurfer/subjects/fsaverage/surf/lh.white
Done reading source surface
Reading annotation
/isilon/work/FBIP/0_projects/freesurfer/subjects/fsaverage/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
mri_read(): couldn't determine type of file
/isilon/work/FBIP/0_projects/PROJECT/GROUP_27SUB/fsaverage.lh/c1/g2v0.weight/high+low/sig.w
ERROR: could not read sig.w as type
At 2014-12-03 13:03:45, "Douglas Greve" <gr...@nmr.mgh.harvard.edu> wrote:
That is the right command line. What is the terminal output?
On 12/2/14 8:01 AM, wangzhiwei3233 wrote:
Hi Freesurfer experts,
I just want to try cluster level threshold by cluster size, but not by mc
simulation.
So I tried the command like : mri_surfcluster --in sig.nii.gz --subject
fsaverage --hemi lh --annot aparc --sign pos --minarea 50 --sum
area50.pos.cluster.summary --o area50.pos.cluster.nii.gz --thmin 1.3
However, I found that the command did not set the non-cluster vertices to
zero.
The help of mri_surfcluster says that this command currently only supports
paint (or w) format for input and output. I converted the sig.nii.gz to sig.w
using
mri_surf2surf --s fsaverage --hemi lh --sval sig.nii.gz --tval sig.w
--trg_type paint.
But command mri_surfcluster could not read the paint file.
Could anyone help me?
Thanks!
Zhiwei
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