What is that input file? It looks like a mask of some part of the brain
On 03/03/2017 06:14 PM, Redwan Maatoug 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 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 > <mailto: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 > <mailto: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 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> > _______________________________________________ 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. 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> . 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 -- 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
