[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

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 rea

Re: [Freesurfer] label2annot issue

bly 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 > > >

Re: [Freesurfer] label2annot issue

hem 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=0BxeTLKLWIP9OeFBa

Re: [Freesurfer] label2annot issue

urfer/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 <redwanm

Re: [Freesurfer] Extract coordinates from .mgh file

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: > >

Re: [Freesurfer] MNI coordinates

n 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 li

[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] 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

Re: [Freesurfer] mri_vol2surf

nmax .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.mg

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

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

[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*

Re: [Freesurfer] mri_vol2surf

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. >

Re: [Freesurfer] mri_vol2surf

t; > 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 nee

[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 :