Re: [Freesurfer] label2annot issue

Yes, send me two label files and the ctab again.

On 8/4/17 12:49 PM, Redwan Maatoug wrote:

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" <greve@nmr.mgh.harvard.edu mailto: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>
<mailto: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>
>   
 <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>>
>     <mailto: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
>     >
>     >
>     >
>     >
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>     MGH-NMR Center
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