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 <gr...@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 > > <redwanmaat...@gmail.com <mailto:redwanmaat...@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 > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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