On Aug 3, 2017 15:40, "Douglas N Greve" <greve@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
> <greve@nmr.mgh.harvard.edu <mailto: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
> <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>
> <mailto: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
> >
> >
> >
> >
> > _______________________________________________
> > 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
> greve@nmr.mgh.harvard.edu <mailto:greve@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:Freesurfer@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
greve@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