It may have to do with the label names that get created from the ctab.
What are the names of the labels in Yeo_split_surf/ ? I can't figure out
what you are doing with that code. Looks like you have broken the yeo
atlas into labels, then you're combining them together again?


On 08/03/2017 05:57 PM, Redwan Maatoug wrote:
> 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 <mailto: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
>
>
>
>

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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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