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. >> >> >
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