In the Yeo_split_surf/ the label have exactly the same names as in the ctab.
They are named like that : parcel_1.mgh-0001.label parcel_2.mgh-0001.label parcel_3.mgh-0001.label ... parcel_112.mgh-0001.label
Yes we had to split the Yeo_split_surface because the goal was to do some analyzes in fMRI and EEG using the same atlas. We had to split the atlas when for example the ROI was crossing the medial line etc...
But now I just want to combine the files again so it is not supposed to have overlapping no ?
Thank you, Redwan
On Thu, Aug 3, 2017 at 3:21 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
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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