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
Please send your full command line, terminal output, and the ctabfile
On 08/03/2017 04:30 PM, Redwan Maatoug 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
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 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
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 <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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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 <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 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
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.
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. 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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 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 thectab.
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>
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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 > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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> > <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> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://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> > <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> > <http://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/> > <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> <mailto: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> > <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> > <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 <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>
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Thank you very much Doug, I really appreciate your help and your patience,
General purpose : in total I have 112.*nii* that I tried to convert them to 112.*mgh* files and then to combined them in a *.annot* file with different colors.
FIRST ISSUE : When I have converted the files from volumetric to surface, I have used this command line : *mri_vol2surf --mov parcel_1.nii **--reg MNI152_T1_brain.dat --hemi lh --o * *parcel_1.mgh*
So this command line worked for 60 files on 112 files but for some of them (for example *parcel_1.nii*) after the conversion the .MGH file seems to be empty.
Because when I use the command line mri_surfcluster to extract the coordinates of the vertices : (*mri_surfcluster --in parcel_1.mgh --hemi lh --subject fsaverage --thmin 0 --nofixmni --olab parcel_1.mgh*) the label file is empty.
when I want to display the .MGH file with the following command line I do not see anything : *tksurfer fsaverage lh inflated -overlay parcel_1.mgh **-fminmax .5 1 *
BUT when i display the .NIFTI file like that : *tkmeditfv fsaverage orig.mgz -overlay parcel_1.nii **-surfs -fminmax .5 1* I see something
First could you tell me why for some files I can convert them from .NII to .MGH but not for all of them.
SECOND ISSUE : For the files, I have successfully converted (because with mri_surfcluster I have vertices coordinates in the label files : like parcel_97.mgh and parcel_100.mgh), could you please tell the steps to follow to display a combined .annot file on tksurfer.
Please find attached : -parcel_1.nii (issue to convert from .nii to .mgh) -parcel_1.mgh (I have the feeling that it is empty) -brain template in MNI 152 space I have used for mri_vol2surf -parcel_97.mgh and parcel_100.mgh (i can't display them as a combined .annot file in tksufer) -the ctab with all the colors for the different parcels.
Thank you very very much, Redwan
On Fri, Aug 4, 2017 at 9:52 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
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 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 thectab.
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 theyeo
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 --ctabcolor.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 playedwith
> --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>
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Doug, did you receive my files? I received an email explaining that the mail is too big and I need to wait for an authorisation from the moderator.
Thank you, Redwan
On Aug 4, 2017 10:34 AM, "Redwan Maatoug" redwanmaatoug@gmail.com wrote:
Thank you very much Doug, I really appreciate your help and your patience,
General purpose : in total I have 112.*nii* that I tried to convert them to 112.*mgh* files and then to combined them in a *.annot* file with different colors.
FIRST ISSUE : When I have converted the files from volumetric to surface, I have used this command line : *mri_vol2surf --mov parcel_1.nii **--reg MNI152_T1_brain.dat --hemi lh --o **parcel_1.mgh*
So this command line worked for 60 files on 112 files but for some of them (for example *parcel_1.nii*) after the conversion the .MGH file seems to be empty.
Because when I use the command line mri_surfcluster to extract the coordinates of the vertices : (*mri_surfcluster --in parcel_1.mgh --hemi lh --subject fsaverage --thmin 0 --nofixmni --olab parcel_1.mgh*) the label file is empty.
when I want to display the .MGH file with the following command line I do not see anything : *tksurfer fsaverage lh inflated -overlay parcel_1.mgh **-fminmax .5 1 *
BUT when i display the .NIFTI file like that : *tkmeditfv fsaverage orig.mgz -overlay parcel_1.nii **-surfs -fminmax .5 1* I see something
First could you tell me why for some files I can convert them from .NII to .MGH but not for all of them.
SECOND ISSUE : For the files, I have successfully converted (because with mri_surfcluster I have vertices coordinates in the label files : like parcel_97.mgh and parcel_100.mgh), could you please tell the steps to follow to display a combined .annot file on tksurfer.
Please find attached : -parcel_1.nii (issue to convert from .nii to .mgh) -parcel_1.mgh (I have the feeling that it is empty) -brain template in MNI 152 space I have used for mri_vol2surf -parcel_97.mgh and parcel_100.mgh (i can't display them as a combined .annot file in tksufer) -the ctab with all the colors for the different parcels.
Thank you very very much, Redwan
On Fri, Aug 4, 2017 at 9:52 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
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 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 thectab.
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 theyeo
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 .mghfiles :
> > *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 --ctabcolor.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 playedwith
> --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>
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