External Email - Use Caution Thanks Bruce!
I even tried with --regheader mri_compute_volume_fractions mri/aseg.mgz --o test --regheader identity.nofile It gives me below error, arg = 6 reading registration file mri/aseg.mgz regio_read_register(): Success Error reading inplaneres from mri/aseg.mgz regio_read_register(): Success Error reading inplaneres from mri/aseg.mgz mri_compute_volume_fractions: could not load registration file from mri/aseg.mgz Thanks, Dhivya ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, April 25, 2018 6:01 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions oh, this must be Doug's code, not mine. Try using --regheader instead And also please send us the full command and all screen output from it in the future. cheers Bruce On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: > External Email - Use Caution > > Sorry for bothering with more questions! > > I am getting an error saying , > > mri_compute_volume_fractions: could not load registration file from > identity.nofile > > And my command is, > > mri_compute_volume_fractions identity.nofile mri/aseg.mgz test > > and if I try to give in this format which the documentation says, > > mri_compute_volume_fractions [options] --o <outstem> --reg <regfile> > > Am I going wrong somewhere? > > Thanks, > Dhivya > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Wednesday, April 25, 2018 4:22 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] mri_compute_volume_fractions > > Hi Dhivya > > if you are doing it in the space of the anatomicals, then use > identity.nofile as the reg file (which is a special file name that will > internally create an identity matrix). The output stem is whatever you > pick - it will be prepended to the files that are written with the volume > fractions. > > cheers > Bruce > On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: > >> External Email - Use Caution >> >> Hi, >> >> I would like to get CSF/GM/WM segmentations from aseg.mgz or in other words >> from labeled brain. Can I do that with mri_compute_volume_fractions ? Also, >> I am not sure about the parameters to supply, >> <reg file> and <output stem>? >> >> Could Someone point me to some documentation on how should use this function >> to get the segmentations ? >> >> Thanks, >> Dhivya >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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
