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 ($session) set to: surfer: /usr/local/freesurfer/subjects checking for nofix files in 'inflated' Reading image info (/usr/local/freesurfer/subjects/fsaverage) Reading /usr/local/freesurfer/subjects/fsaverage/mri/orig.mgz surfer: Reading header info from /usr/local/freesurfer/subjects/fsaverage/mri/orig.mgz surfer: vertices=163842, faces=327680 reading colortable from annotation file... colortable with 113 entries read (originally none) Found embedded color table in annotation. surfer: single buffered window surfer: tkoInitWindow(fsaverage) setting percentile thresholds (-1.00, 0.00, 0.00) surfer: using interface /usr/local/freesurfer/tktools/tksurfer.tcl Reading /usr/local/freesurfer/tktools/tkm_common.tcl Reading /usr/local/freesurfer/tktools/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/tktools/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... Thank you very much, Redwan On Thu, Aug 3, 2017 at 1:30 PM, Redwan Maatoug <[email protected]> wrote: > Hi all, > > So my issue is the following : > > I have 112 mgh files. (They come from the Yeo 17 Network atlas (we split > the atlas in smaller regions). I have extracted the coordinates with : > mri_surfcluster (playing with the thmin option) > mri_vol2label > > and then I have used mri_label2annot with my own color lookup table to > combine the 112 files into 1 file. (I have played with --noverbose, > --maxstatwinner) > > When I try to display, I have the feeling that there is some overlapping > because what tksufer dispays, is not very relevant and it is spotty. > > I have attached some screenshots > Thank you very much for your help, > Redwan >
#$Id: FreeSurferColorLUT.txt,v 1.38.2.1 2007/08/20 01:52:07 nicks Exp $ #No. Label Name: R G B A 0 Unknown 255 255 255 0 1 parcel_1.mgh-0001.label 0 0 0 0 2 parcel_97.mgh-0001.label 0 0 0 0 3 parcel_2.mgh-0001.label 255 255 0 0 4 parcel_98.mgh-0001.label 255 255 0 0 5 parcel_3.mgh-0001.label 255 0 0 0 6 parcel_4.mgh-0001.label 255 0 0 0 7 parcel_5.mgh-0001.label 255 0 0 0 8 parcel_99.mgh-0001.label 255 0 0 0 9 parcel_6.mgh-0001.label 0 0 255 0 10 parcel_7.mgh-0001.label 0 0 255 0 11 parcel_8.mgh-0001.label 0 255 255 0 12 parcel_9.mgh-0001.label 0 255 255 0 13 parcel_10.mgh-0001.label 0 255 255 0 14 parcel_11.mgh-0001.label 0 255 255 0 15 parcel_12.mgh-0001.label 255 0 255 0 16 parcel_13.mgh-0001.label 255 0 255 0 17 parcel_14.mgh-0001.label 255 0 255 0 18 parcel_15.mgh-0001.label 255 0 255 0 19 parcel_16.mgh-0001.label 255 0 255 0 20 parcel_17.mgh-0001.label 255 0 255 0 21 parcel_18.mgh-0001.label 255 0 255 0 22 parcel_100.mgh-0001.label 255 0 255 0 23 parcel_19.mgh-0001.label 0 255 0 0 24 parcel_20.mgh-0001.label 0 255 0 0 25 parcel_21.mgh-0001.label 0 255 0 0 26 parcel_22.mgh-0001.label 0 255 0 0 27 parcel_23.mgh-0001.label 0 255 0 0 28 parcel_24.mgh-0001.label 0 255 0 0 29 parcel_25.mgh-0001.label 0 255 0 0 30 parcel_26.mgh-0001.label 0 255 0 0 31 parcel_27.mgh-0001.label 0 255 0 0 32 parcel_101.mgh-0001.label 0 255 0 0 33 parcel_28.mgh-0001.label 255 171 0 0 34 parcel_29.mgh-0001.label 255 171 0 0 35 parcel_30.mgh-0001.label 255 171 0 0 36 parcel_31.mgh-0001.label 255 171 0 0 37 parcel_32.mgh-0001.label 255 171 0 0 38 parcel_33.mgh-0001.label 255 171 0 0 39 parcel_34.mgh-0001.label 255 171 0 0 40 parcel_35.mgh-0001.label 255 171 0 0 41 parcel_36.mgh-0001.label 255 171 0 0 42 parcel_37.mgh-0001.label 255 171 0 0 43 parcel_38.mgh-0001.label 255 171 0 0 44 parcel_39.mgh-0001.label 255 171 0 0 45 parcel_102.mgh-0001.label 255 171 0 0 46 parcel_40.mgh-0001.label 0 255 171 0 47 parcel_41.mgh-0001.label 0 255 171 0 48 parcel_42.mgh-0001.label 102 0 102 0 49 parcel_103.mgh-0001.label 102 0 102 0 50 parcel_43.mgh-0001.label 153 153 255 0 51 parcel_44.mgh-0001.label 153 153 255 0 52 parcel_45.mgh-0001.label 153 153 255 0 53 parcel_104.mgh-0001.label 153 153 255 0 54 parcel_105.mgh-0001.label 153 153 255 0 55 parcel_46.mgh-0001.label 153 255 153 0 56 parcel_47.mgh-0001.label 153 255 153 0 57 parcel_48.mgh-0001.label 153 255 153 0 58 parcel_49.mgh-0001.label 153 255 153 0 59 parcel_50.mgh-0001.label 153 255 153 0 60 parcel_51.mgh-0001.label 153 255 153 0 61 parcel_52.mgh-0001.label 153 255 153 0 62 parcel_53.mgh-0001.label 153 255 153 0 63 parcel_54.mgh-0001.label 153 255 153 0 64 parcel_55.mgh-0001.label 153 255 153 0 65 parcel_106.mgh-0001.label 153 255 153 0 66 parcel_107.mgh-0001.label 153 255 153 0 67 parcel_56.mgh-0001.label 153 76 0 0 68 parcel_57.mgh-0001.label 153 76 0 0 69 parcel_58.mgh-0001.label 153 76 0 0 70 parcel_59.mgh-0001.label 153 76 0 0 71 parcel_60.mgh-0001.label 153 76 0 0 72 parcel_61.mgh-0001.label 153 76 0 0 73 parcel_62.mgh-0001.label 153 76 0 0 74 parcel_63.mgh-0001.label 153 76 0 0 75 parcel_64.mgh-0001.label 153 76 0 0 76 parcel_65.mgh-0001.label 153 76 0 0 77 parcel_66.mgh-0001.label 153 76 0 0 78 parcel_67.mgh-0001.label 153 76 0 0 79 parcel_108.mgh-0001.label 153 76 0 0 80 parcel_68.mgh-0001.label 102 102 255 0 81 parcel_69.mgh-0001.label 102 102 255 0 82 parcel_70.mgh-0001.label 102 102 255 0 83 parcel_71.mgh-0001.label 102 102 255 0 84 parcel_72.mgh-0001.label 102 102 255 0 85 parcel_73.mgh-0001.label 153 255 51 0 86 parcel_74.mgh-0001.label 153 255 51 0 87 parcel_75.mgh-0001.label 153 255 51 0 88 parcel_76.mgh-0001.label 153 255 51 0 89 parcel_77.mgh-0001.label 153 255 51 0 90 parcel_109.mgh-0001.label 153 255 51 0 91 parcel_78.mgh-0001.label 255 229 4 0 92 parcel_79.mgh-0001.label 255 229 4 0 93 parcel_80.mgh-0001.label 255 229 4 0 94 parcel_81.mgh-0001.label 255 229 4 0 95 parcel_82.mgh-0001.label 255 229 4 0 96 parcel_83.mgh-0001.label 255 229 4 0 97 parcel_84.mgh-0001.label 255 229 4 0 98 parcel_85.mgh-0001.label 255 229 4 0 99 parcel_86.mgh-0001.label 255 229 4 0 100 parcel_87.mgh-0001.label 255 229 4 0 101 parcel_110.mgh-0001.label 255 229 4 0 102 parcel_111.mgh-0001.label 255 229 4 0 103 parcel_88.mgh-0001.label 0 51 25 0 104 parcel_89.mgh-0001.label 0 51 25 0 105 parcel_90.mgh-0001.label 0 51 25 0 106 parcel_91.mgh-0001.label 0 51 25 0 107 parcel_92.mgh-0001.label 0 51 25 0 108 parcel_93.mgh-0001.label 0 51 25 0 109 parcel_94.mgh-0001.label 0 51 25 0 110 parcel_95.mgh-0001.label 0 51 25 0 111 parcel_96.mgh-0001.label 0 51 25 0 112 parcel_112.mgh-0001.label 0 51 25 0
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