[Freesurfer] Sphere above a certain vetex
Hi everybody, I have a .annot file and I would like to display a sphere above one certain vertex. (I know the coordinates of the vertex) Someone knows a way to do that ? Thank you very much, Redwan ___ 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.
Re: [Freesurfer] label2annot issue
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" <redwanmaat...@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 <gr...@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" <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 o
Re: [Freesurfer] label2annot issue
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=1.00 (1.00), thmax=-1.00 (-1), thsignid=0,
> > > minarea=5.00
> > > 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) ---
> > >
> > /us
Re: [Freesurfer] label2annot issue
In the Yeo_split_surf/ the label have exactly the same names as in the ctab.
They are named like that :
parcel_1.mgh-0001.label
parcel_2.mgh-0001.label
parcel_3.mgh-0001.label
...
parcel_112.mgh-0001.label
Yes we had to split the Yeo_split_surface because the goal was to do some
analyzes in fMRI and EEG using the same atlas. We had to split the atlas
when for example the ROI was crossing the medial line etc...
But now I just want to combine the files again so it is not supposed to
have overlapping no ?
Thank you,
Redwan
On Thu, Aug 3, 2017 at 3:21 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> It may have to do with the label names that get created from the ctab.
> What are the names of the labels in Yeo_split_surf/ ? I can't figure out
> what you are doing with that code. Looks like you have broken the yeo
> atlas into labels, then you're combining them together again?
>
>
> On 08/03/2017 05:57 PM, Redwan Maatoug wrote:
> > Thank you ffor your quick answer,
> >
> > I have attached the --ctab
> >
> > Here is the link for the .mgh files.
> >
> > https://drive.google.com/open?id=0BxeTLKLWIP9OeFBaQm9iYVRfYVE
> >
> >
> > So my command line to extract the coordinates from the .mgh files :
> >
> > *I)*
> > for f in ${1}/*.mgh
> > do
> > mri_surfcluster --in ${f} --hemi lh --subject fsaverage --thmin 0
> > --nofixmni --olab ./${f}
> > done
> >
> > _#OUTPUT for 1 file #_
> > Reading source surface
> > /usr/local/freesurfer/subjects/fsaverage/surf/lh.white
> > Done reading source surface
> > Computing metric properties
> > Loading source values
> > number of voxels in search space = 163842
> > Done loading source values (nvtxs = 163842)
> > overall max = 1 at vertex 0
> > overall min = 0 at vertex 1
> > surface nvertices 163842
> > metric props tot surface area 65416.984375
> > group_avg_vtxarea_loaded 1
> > masked surface area 82219.390625
> > NOT Adjusting threshold for 1-tailed test
> > thminadj = 1
> > Searching for Clusters ...
> > thmin=1.00 (1.00), thmax=-1.00 (-1), thsignid=0,
> > minarea=5.00
> > 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
> > 1.0 0.0 0.0 0.0;
> > 0.0 1.0 0.0 0.0;
> > 0.0 0.0 1.0 0.0;
> > 0.0 0.0 0.0 1.0;
> >
> > 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=1.00 (1.00), thmax=-1.00 (-1), thsignid=0,
> > minarea=5.00
> > 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/
> >
> > sysna
Re: [Freesurfer] label2annot issue
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=1.00 (1.00), thmax=-1.00 (-1), thsignid=0,
minarea=5.00
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
1.0 0.0 0.0 0.0;
0.0 1.0 0.0 0.0;
0.0 0.0 1.0 0.0;
0.0 0.0 0.0 1.0;
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=1.00 (1.00), thmax=-1.00 (-1), thsignid=0,
minarea=5.00
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
hemilh
SUBJECTS_DIR /usr/local/freesurfer/subjects
ColorTable color.txt
AnnotName combined
nlables 0
LabelThresh 0 0.00
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
hemiis 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>
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 regio
Re: [Freesurfer] Extract coordinates from .mgh file
Hi Doug, Thank you for your reply, I have used the tool *surf_cluster* to have the MNI coordinates. Is it a good alternative to *mri_cor2label *? Thank you very much, Regards, Redwan On Wed, Jul 26, 2017 at 2:41 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > mri_cor2label with extract the coordinates into a label file. The > coordinates will be in "tkregisterRAS". What coordinate system do you > want? See > > See https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems > > > On 07/25/2017 07:32 PM, Redwan Maatoug wrote: > > Hi experts, > > > > I just want to know a way to extract the coordinates from a ROI mgh file. > > > > I know that I can load the file with tksurfer but I have 100 .mgh > > files so if I could run a command line to have the coordinates in a > > .txt file or in a .m it would be helpful. > > > > Thank you, > > Redwan > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ 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.
Re: [Freesurfer] MNI coordinates
It is exactly what I want, Thank you for your responsiveness and for your help, Redwan On Wed, Jul 26, 2017 at 12:14 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > If you run it with --nofixmni, it will report MNI305 coords. Is that > what you want? > > > On 07/26/2017 03:11 PM, Redwan Maatoug wrote: > > Hi all, > > > > My goal is to extract the coordinates from a .mgh ROI surface file. > > > > I have used this tool : > > mri_surfcluster with > > > > But the coordinates are in Tailarch and I would like the *MNI > > coordinates*. Someone has an idea ? > > > > Thank you, > > Redwan > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ 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.
[Freesurfer] MNI coordinates
Hi all, My goal is to extract the coordinates from a .mgh ROI surface file. I have used this tool : mri_surfcluster with But the coordinates are in Tailarch and I would like the *MNI coordinates*. Someone has an idea ? Thank you, Redwan ___ 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.
[Freesurfer] Extract coordinates from .mgh file
Hi experts, I just want to know a way to extract the coordinates from a ROI mgh file. I know that I can load the file with tksurfer but I have 100 .mgh files so if I could run a command line to have the coordinates in a .txt file or in a .m it would be helpful. Thank you, Redwan ___ 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.
Re: [Freesurfer] mri_vol2surf
Thank you very much Douglas, You made my day ! Have a good day, Redwan On 14 March 2017 at 10:48, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > Yes, I see a spot on the medial wall. You can also look at it in the > volume with > > tkmeditfv fsaverage orig.mgz -surfs -fminmax .5 1 -overlay > multdemand_MCC_SMA_thr50.nii.gz --reg MNI152.dat > > On 3/14/17 1:45 PM, Redwan Maatoug wrote: > > Hi Bruce, > > Yes, I did. > Do you see something ? > > Thank you, > Redwan > > On 14 March 2017 at 09:19, Douglas Greve <gr...@nmr.mgh.harvard.edu> > wrote: > >> did you look at the medial wall? >> >> On 3/13/17 8:48 PM, Redwan Maatoug wrote: >> >> Thank you very much Douglas, >> >> I think that I probably miss something. >> There is no error in the terminal but when i launch tksurfer, I have the >> following screenshot (screen1). The overlay is loaded but the coordinates >> are 0.0 and the overlay is not in a different color that the brain. >> I have attached, in case, the brain file and the volumetric file. >> >> As you can see, I have followed all the instructions : >> >> 1) bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg >> MNI152.dat --t1 --init-coreg >> >> 2) mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg MNI152.dat >> --hemi lh --o ./multidem.mgh >> >> 3) tksurfer fsaverage lh inflated -overlay multidem.mgh -fminmax .5 1 >> >> Thank you, >> Best, >> >> Redwan Maatoug >> Resident in psychiatry >> Stanford University >> Amit Etkin lab >> >> On 13 March 2017 at 14:51, Douglas N Greve <gr...@nmr.mgh.harvard.edu> >> wrote: >> >>> The file you created is not a label so don't try to load it with -label. >>> Instead use -overlay file.mgh -fminmax .5 1 >>> >>> >>> >>> On 03/13/2017 05:40 PM, Redwan Maatoug wrote: >>> > Hi Douglas, >>> > >>> > Sorry to bother you, again. >>> > Actually, my command was t1 and not t2 but even with t1 nothing works. >>> > So if my command line is exact, do you think it is a problem with my >>> > files ? >>> > >>> > Thank you, >>> > >>> > Redwan Maatoug >>> > Resident in psychiatry >>> > Stanford University >>> > Amit Etkin lab >>> > >>> > On 13 March 2017 at 13:41, Douglas N Greve <gr...@nmr.mgh.harvard.edu >>> > <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>> > >>> > Use --t1 (I assume the --tw was supposed to be --t2, which is >>> > wrong for >>> > that mni152 volume) >>> > >>> > >>> > On 03/09/2017 08:58 PM, Redwan Maatoug wrote: >>> > > Hi Douglas, >>> > > >>> > > Indeed you have already helped me ! >>> > > Thank you for your help and for your time. >>> > > >>> > > I have tried to do, as you said. >>> > > I have used the brain image for the registration and then I have >>> > > tried to convert my ROI nifti volumetric file into a surface file >>> > > using this registration file. >>> > > >>> > > I do not know what is wrong with my command line and I tried >>> > many many >>> > > things. >>> > > >>> > > I have attached two files >>> > > (MNI152_T1_2mm_brain.nii is the brain file, >>> > > multdemand_MCC_SMA_thr50.nii.gz is the ROI file). >>> > > >>> > > I have tried the following commands : >>> > > 1) *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg >>> > > MNI152.dat --tw --init-coreg* >>> > > >>> > > 2) *mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg >>> > > MNI152.dat --hemi lh --o ./multidem.mgh* >>> > > >>> > > I do not know if the output format .mgh is correct. >>> > > Anyway when I launch it with : >>> > > *tksurfer fsaverage lh inflated -label multidem.mgh* >>> > > >>> > > the multidem.mgh file does not appear. >>> > > >>> > > Thank you by advance for your advice, >>> > > Best, >>> > > Redwan >>> > > >>> > > On 9 March 2017 at 09:09, Dougl
Re: [Freesurfer] mri_vol2surf
Hi Bruce, Yes, I did. Do you see something ? Thank you, Redwan On 14 March 2017 at 09:19, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > did you look at the medial wall? > > On 3/13/17 8:48 PM, Redwan Maatoug wrote: > > Thank you very much Douglas, > > I think that I probably miss something. > There is no error in the terminal but when i launch tksurfer, I have the > following screenshot (screen1). The overlay is loaded but the coordinates > are 0.0 and the overlay is not in a different color that the brain. > I have attached, in case, the brain file and the volumetric file. > > As you can see, I have followed all the instructions : > > 1) bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg MNI152.dat > --t1 --init-coreg > > 2) mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg MNI152.dat > --hemi lh --o ./multidem.mgh > > 3) tksurfer fsaverage lh inflated -overlay multidem.mgh -fminmax .5 1 > > Thank you, > Best, > > Redwan Maatoug > Resident in psychiatry > Stanford University > Amit Etkin lab > > On 13 March 2017 at 14:51, Douglas N Greve <gr...@nmr.mgh.harvard.edu> > wrote: > >> The file you created is not a label so don't try to load it with -label. >> Instead use -overlay file.mgh -fminmax .5 1 >> >> >> >> On 03/13/2017 05:40 PM, Redwan Maatoug wrote: >> > Hi Douglas, >> > >> > Sorry to bother you, again. >> > Actually, my command was t1 and not t2 but even with t1 nothing works. >> > So if my command line is exact, do you think it is a problem with my >> > files ? >> > >> > Thank you, >> > >> > Redwan Maatoug >> > Resident in psychiatry >> > Stanford University >> > Amit Etkin lab >> > >> > On 13 March 2017 at 13:41, Douglas N Greve <gr...@nmr.mgh.harvard.edu >> > <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> > >> > Use --t1 (I assume the --tw was supposed to be --t2, which is >> > wrong for >> > that mni152 volume) >> > >> > >> > On 03/09/2017 08:58 PM, Redwan Maatoug wrote: >> > > Hi Douglas, >> > > >> > > Indeed you have already helped me ! >> > > Thank you for your help and for your time. >> > > >> > > I have tried to do, as you said. >> > > I have used the brain image for the registration and then I have >> > > tried to convert my ROI nifti volumetric file into a surface file >> > > using this registration file. >> > > >> > > I do not know what is wrong with my command line and I tried >> > many many >> > > things. >> > > >> > > I have attached two files >> > > (MNI152_T1_2mm_brain.nii is the brain file, >> > > multdemand_MCC_SMA_thr50.nii.gz is the ROI file). >> > > >> > > I have tried the following commands : >> > > 1) *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg >> > > MNI152.dat --tw --init-coreg* >> > > >> > > 2) *mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg >> > > MNI152.dat --hemi lh --o ./multidem.mgh* >> > > >> > > I do not know if the output format .mgh is correct. >> > > Anyway when I launch it with : >> > > *tksurfer fsaverage lh inflated -label multidem.mgh* >> > > >> > > the multidem.mgh file does not appear. >> > > >> > > Thank you by advance for your advice, >> > > Best, >> > > Redwan >> > > >> > > On 9 March 2017 at 09:09, Douglas N Greve >> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> > > <mailto:gr...@nmr.mgh.harvard.edu >> > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: >> > > >> > > didn't I respond to this earlier this week? the images >> > appear to be >> > > binarized regions of interest and not whole (or ever partial) >> > > brain. To >> > > run the registration, you will need an actual brain. If you >> > > created the >> > > ROI from a brain image, then use that image to create the reg, >> > > then run >> > > vol2surf using that reg with the ROI as input >> > > >> > > &
Re: [Freesurfer] mri_vol2surf
Hi Douglas, Sorry to bother you, again. Actually, my command was t1 and not t2 but even with t1 nothing works. So if my command line is exact, do you think it is a problem with my files ? Thank you, Redwan Maatoug Resident in psychiatry Stanford University Amit Etkin lab On 13 March 2017 at 13:41, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > Use --t1 (I assume the --tw was supposed to be --t2, which is wrong for > that mni152 volume) > > > On 03/09/2017 08:58 PM, Redwan Maatoug wrote: > > Hi Douglas, > > > > Indeed you have already helped me ! > > Thank you for your help and for your time. > > > > I have tried to do, as you said. > > I have used the brain image for the registration and then I have > > tried to convert my ROI nifti volumetric file into a surface file > > using this registration file. > > > > I do not know what is wrong with my command line and I tried many many > > things. > > > > I have attached two files > > (MNI152_T1_2mm_brain.nii is the brain file, > > multdemand_MCC_SMA_thr50.nii.gz is the ROI file). > > > > I have tried the following commands : > > 1) *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg > > MNI152.dat --tw --init-coreg* > > > > 2) *mri_vol2surf --mov multdemand_MCC_SMA_thr50.nii.gz --reg > > MNI152.dat --hemi lh --o ./multidem.mgh* > > > > I do not know if the output format .mgh is correct. > > Anyway when I launch it with : > > *tksurfer fsaverage lh inflated -label multidem.mgh* > > > > the multidem.mgh file does not appear. > > > > Thank you by advance for your advice, > > Best, > > Redwan > > > > On 9 March 2017 at 09:09, Douglas N Greve <gr...@nmr.mgh.harvard.edu > > <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > > didn't I respond to this earlier this week? the images appear to be > > binarized regions of interest and not whole (or ever partial) > > brain. To > > run the registration, you will need an actual brain. If you > > created the > > ROI from a brain image, then use that image to create the reg, > > then run > > vol2surf using that reg with the ROI as input > > > > > > On 03/07/2017 03:02 PM, Redwan Maatoug wrote: > > > Hi experts, > > > > > > I try to convert my volumetric nifti file to surface files. > > > > > > My nifti volumetric file looks like : 1. screenshot > > > I have first registered the volumetric file using bbregister > > with this > > > command line : > > > *bbregister --s fsaverage --mov segment_7.nii --reg > > segment_7.dat --t1 > > > --init-coreg* > > > > > > then I have used the following command line and the file looks like > > > screenshot 1 attached : > > > *tkregister2 --mov segment_7.nii --reg register7.dat --surf* > > > > > > And after that, I have tried to convert my volumetric file to > > surface > > > file with this command line : > > > > > > *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi > > lh --o > > > ./segment_7-lh.nii --float2int round* > > > > > > But with this command when I load the file with freeview it does > not > > > work and with tkregister the file is empty. > > > > > > Or this one : > > > > > > *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi > > lh --o > > > ./segment_7-lh.w --out_type paint --float2int tkregister* > > > > > > But with this command I have this warning : > > > Warning: all vertex values are zero > > > > > > Could you please help me to convert my volumetric files because I > am > > > probably doing someting wrong. All my files come from an Atlas and > I > > > just need to convert them to surfaces files. > > > > > > Thank you 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. >
[Freesurfer] mri_vol2surf
Hi experts, I try to convert my volumetric nifti file to surface files. My nifti volumetric file looks like : 1. screenshot I have first registered the volumetric file using bbregister with this command line : *bbregister --s fsaverage --mov segment_7.nii --reg segment_7.dat --t1 --init-coreg* then I have used the following command line and the file looks like screenshot 1 attached : *tkregister2 --mov segment_7.nii --reg register7.dat --surf* And after that, I have tried to convert my volumetric file to surface file with this command line : *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o ./segment_7-lh.nii --float2int round* But with this command when I load the file with freeview it does not work and with tkregister the file is empty. Or this one : *mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o ./segment_7-lh.w --out_type paint --float2int tkregister* But with this command I have this warning : Warning: all vertex values are zero Could you please help me to convert my volumetric files because I am probably doing someting wrong. All my files come from an Atlas and I just need to convert them to surfaces files. Thank you for your help, Redwan ___ 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.
Re: [Freesurfer] mri_vol2surf
Hi Douglas, Thank you for your help, So I still can't convert my volumetric file to a surface file and I don't know what I am doing wrong. My nifti volumetric file looks like : 1. screenshot As you said, i have first registered the volumetric file using bbregister. I have used this command line : tkregister2 --mov segment_7.nii --reg register7.dat --surf (knowing that segment_7.nii is my volumetric file which looks like 1.screenshot). With this command line, my output is this file : 2.screenshot (attached). Am I satisfied with this file ? if not what can I do to improve the result and the matching ? And after that, I have tried to convert my volumetric file to surface file with this command line : mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o ./segment_7-lh.nii --float2int round But with this command when I load the file with freeview it does not work and with tkregister the file is empty. Or this one : mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o ./segment_7-lh.w --out_type paint --float2int tkregister But with this command I have the following warning : Warning: all vertex values are zero Thank you by advance for your precious help, Have a nice day, Redwan On 2 March 2017 at 10:07, Redwan Maatoug <redwanmaat...@gmail.com> wrote: > Hi Douglas, > > Thank you for your help, > > So I still can't convert my volumetric file to a surface file and I don't > know what I am doing wrong. > > My nifti volumetric file looks like : 1. screenshot > As you said, i have first registered the volumetric file > using bbregister. > I have used this command line : > tkregister2 --mov segment_7.nii --reg register7.dat --surf > (knowing that segment_7.nii is my volumetric file which looks like > 1.screenshot). > With this command line, my output is this file : 2.screenshot (attached). > > Am I satisfied with this file ? if not what can I do to improve the result > and the matching ? > > And after that, I have tried to convert my volumetric file to surface file > with this command line : > > mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o > ./segment_7-lh.nii --float2int round > > But with this command when I load the file with freeview it does not work > and with tkregister the file is empty. > > Or this one : > > mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o > ./segment_7-lh.w --out_type paint --float2int tkregister > > But with this command I have this warning : > Warning: all vertex values are zero > > Thank you by advance for your precious help, > Have a nice day, > Redwan > > On 1 March 2017 at 07:31, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > >> Hi Redwan, >> >> You'll need to register your volume to an FS-analyzed data set (probably >> using bbregister). Then apply mri_vol2surf (run with --help to get examples) >> >> doug >> >> On 2/28/17 5:17 PM, Redwan Maatoug wrote: >> >> Hi all ! >> >> I would like to convert my files : volumetrics nifti files to surfaces >> files. >> My volumetrics nifti files come from an Atlas and I would like to convert >> them to surfaces files (i need the surfaces files). >> >> Could you please tell me the process because I have tried many things >> like : >> >> mri_vol2surf --src pathwaytomyfile --hemi lh --float2int round --out >> thepathwayIwantToputmySurfaceFileAfterConversion >> >> And it did not work. >> >> Thank you for your help, >> Redwan >> >> >> >> ___ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> ___ >> 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. >> >> > ___ 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.
Re: [Freesurfer] mri_vol2surf
Hi Douglas, Thank you for your help, So I still can't convert my volumetric file to a surface file and I don't know what I am doing wrong. My nifti volumetric file looks like : 1. screenshot As you said, i have first registered the volumetric file using bbregister. I have used this command line : tkregister2 --mov segment_7.nii --reg register7.dat --surf (knowing that segment_7.nii is my volumetric file which looks like 1.screenshot). With this command line, my output is this file : 2.screenshot (attached). Am I satisfied with this file ? if not what can I do to improve the result and the matching ? And after that, I have tried to convert my volumetric file to surface file with this command line : mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o ./segment_7-lh.nii --float2int round But with this command when I load the file with freeview it does not work and with tkregister the file is empty. Or this one : mri_vol2surf --src segment_7.nii --srcreg register7.dat --hemi lh --o ./segment_7-lh.w --out_type paint --float2int tkregister But with this command I have this warning : Warning: all vertex values are zero Thank you by advance for your precious help, Have a nice day, Redwan On 1 March 2017 at 07:31, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: > Hi Redwan, > > You'll need to register your volume to an FS-analyzed data set (probably > using bbregister). Then apply mri_vol2surf (run with --help to get examples) > > doug > > On 2/28/17 5:17 PM, Redwan Maatoug wrote: > > Hi all ! > > I would like to convert my files : volumetrics nifti files to surfaces > files. > My volumetrics nifti files come from an Atlas and I would like to convert > them to surfaces files (i need the surfaces files). > > Could you please tell me the process because I have tried many things like > : > > mri_vol2surf --src pathwaytomyfile --hemi lh --float2int round --out > thepathwayIwantToputmySurfaceFileAfterConversion > > And it did not work. > > Thank you for your help, > Redwan > > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > ___ > 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. > > ___ 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.
[Freesurfer] mri_vol2surf
Hi all ! I would like to convert my files : volumetrics nifti files to surfaces files. My volumetrics nifti files come from an Atlas and I would like to convert them to surfaces files (i need the surfaces files). Could you please tell me the process because I have tried many things like : mri_vol2surf --src pathwaytomyfile --hemi lh --float2int round --out thepathwayIwantToputmySurfaceFileAfterConversion And it did not work. Thank you for your help, Redwan ___ 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.
