Hi Douglas, I tried to rename the parcel files and in the ctab but it does not change anything. I have the feeling that sometime label2abnot can read the colors because as you can see in the screenshots there is some colors on the brain. If I give you the files could you help me to follow the rights steps to make? Maybe I am missing something but I really need this to be done to compare the résultats in fMRI and in EEG.
Thank you very much, Redwan On Aug 3, 2017 15:40, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: > that would mean that mris_label2annot is probably not reading any of > your labels because it is expecting the label name to be, eg, > lh.parcel_1.mgh-0001.label.label based on what you have told me. Try > changing he label name in the folder to lh.parcel_1.mgh-001.label and > change the ctab names to parcel_1.mgh-0001 > > > On 08/03/2017 06:35 PM, Redwan Maatoug wrote: > > 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 <mailto: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 > > <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> > > <mailto: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 > > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > > Phone Number: 617-724-2358 <tel:617-724-2358> > > Fax: 617-726-7422 <tel:617-726-7422> > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > <https://gate.nmr.mgh.harvard.edu/filedrop2> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:freesur...@nmr.mgh. > harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <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 > > <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. > > > > > > > > > > _______________________________________________ > > 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 >
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