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