Thank you ffor your quick answer,

I have attached the --ctab 

Here is the link for the .mgh files.

https://drive.google.com/open?id=0BxeTLKLWIP9OeFBaQm9iYVRfYVE


So my command line to extract the coordinates from the .mgh files :

I)
for f in ${1}/*.mgh
do 
    mri_surfcluster --in ${f} --hemi lh --subject fsaverage --thmin 0 --nofixmni --olab ./${f}
done

#OUTPUT for 1 file #
Reading source surface /usr/local/freesurfer/subjects/fsaverage/surf/lh.white
Done reading source surface
Computing metric properties
Loading source values
number of voxels in search space = 163842
Done loading source values (nvtxs = 163842)
overall max = 1 at vertex 0
overall min = 0 at vertex 1
surface nvertices 163842
metric props tot surface area 65416.984375
group_avg_vtxarea_loaded 1
masked surface area 82219.390625
NOT Adjusting threshold for 1-tailed test
thminadj = 1
Searching for Clusters ...
thmin=1.000000 (1.000000), thmax=-1.000000 (-1), thsignid=0, minarea=5.000000
Found 3 clusters
Max cluster size 4759.318359
thsign = abs, id = 0
version $Id: mri_surfcluster.c,v 1.57.2.3 2016/11/17 18:19:42 zkaufman Exp $
hemi           = lh
srcid          = Yeo_Split_surf/parcel_9.mgh 
srcsubjid      = fsaverage
srcsurf        = white
srcframe       = 0
thsign         = abs
thmin          = 1
thmax          = -1
fdr            = -1
minarea        = 5
xfmfile        = talairach.xfm
nth         = -1
subjectsdir    = /usr/local/freesurfer/subjects
FixMNI = 0
------------- XFM matrix (RAS2RAS) ---------------
/usr/local/freesurfer/subjects/fsaverage/mri/transforms/talairach.xfm
 1.00000   0.00000   0.00000   0.00000;
 0.00000   1.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000   0.00000   0.00000   1.00000;
----------------------------------------------------
Reading source surface /usr/local/freesurfer/subjects/fsaverage/surf/lh.white
Done reading source surface
Computing metric properties
Loading source values
number of voxels in search space = 163842
Done loading source values (nvtxs = 163842)
overall max = 1 at vertex 4422
overall min = 0 at vertex 0
surface nvertices 163842
metric props tot surface area 65416.984375
group_avg_vtxarea_loaded 1
masked surface area 82219.390625
NOT Adjusting threshold for 1-tailed test
thminadj = 1
Searching for Clusters ...
thmin=1.000000 (1.000000), thmax=-1.000000 (-1), thsignid=0, minarea=5.000000
Found 1 clusters
Max cluster size 16.666323

II)

mris_label2annot --s fsaverage --h lh --a combined --ctab color.txt  --ldir Yeo_split_surf/

I tried without any improvement to add this arguments : --noverbose --thresh 1 --maxstatwinner 


Reading ctab color.txt

Number of ctab entries 113

INFO: no labels specified, generating from ctab

# OUTPUT #

$Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $

cwd /usr/local/freesurfer/subjects

cmdline mris_label2annot --s fsaverage --h lh --a combined --ctab color.txt --ldir Yeo_split_surf/ 

sysname  Linux

hostname redwanmaatoug-MacBookPro

machine  x86_64

user     redwanmaatoug


subject fsaverage

hemi    lh

SUBJECTS_DIR /usr/local/freesurfer/subjects

ColorTable color.txt

AnnotName  combined

nlables 0

LabelThresh 0 0.000000

Loading /usr/local/freesurfer/subjects/fsaverage/surf/lh.orig

Mapping unhit to unknown

Found 163842 unhit vertices

Writing annot to /usr/local/freesurfer/subjects/fsaverage/label/lh.combined.annot


III)

tksurfer fsaverage lh inflated -annotation /usr/local/freesurfer/subjects/fsaverage/label/lh.combined.annot

# OUTPUT #

subject is fsaverage

hemi    is lh

surface is inflated

surfer: current subjects dir: /usr/local/freesurfer/subjects

surfer: not in "scripts" dir ==> using cwd for session root

surfer: session root data dir ($session) set to:

surfer:     /usr/local/freesurfer/subjects

checking for nofix files in 'inflated'

Reading image info (/usr/local/freesurfer/subjects/fsaverage)

Reading /usr/local/freesurfer/subjects/fsaverage/mri/orig.mgz

surfer: Reading header info from /usr/local/freesurfer/subjects/fsaverage/mri/orig.mgz

surfer: vertices=163842, faces=327680

reading colortable from annotation file...

colortable with 113 entries read (originally none)

Found embedded color table in annotation.

surfer: single buffered window

surfer: tkoInitWindow(fsaverage)

setting percentile thresholds (-1.00, 0.00, 0.00)

surfer: using interface /usr/local/freesurfer/tktools/tksurfer.tcl

Reading /usr/local/freesurfer/tktools/tkm_common.tcl

Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl

Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl

Reading /usr/local/freesurfer/tktools/tkUtils.tcl

Successfully parsed tksurfer.tcl

reading white matter vertex locations...



Thank you very much,


Redwan 

On Thu, Aug 3, 2017 at 1:30 PM, Redwan Maatoug <redwanmaatoug@gmail.com> wrote:
Hi all,

So my issue is the following :

I have 112 mgh files. (They come from the Yeo 17 Network atlas (we split the atlas in smaller regions). I have extracted the coordinates with :
mri_surfcluster (playing with the thmin option)
mri_vol2label 

and then I have used mri_label2annot with my own color lookup table to combine the 112 files into 1 file. (I have played with --noverbose, --maxstatwinner)

When I try to display, I have the feeling that there is some overlapping because what tksufer dispays, is not very relevant and it is spotty. 

I have attached some screenshots 
Thank you very much for your help,
Redwan