External Email - Use Caution mri_compute_volume_fractions --o test --regheader unknown option --o
If I am not giving any input before arguments, it is not taking them. 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: Thursday, April 26, 2018 10:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions just run the command as I sent it: mri_compute_volume_fractions --o test --regheader the aseg is the default name. You are putting it in the wrong place and it thinks the aseg is a registration file On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote: > External Email - Use Caution > > I am getting same Error with many permutations of arguments, > > mri_compute_volume_fractions 002_S/mri/aseg.mgz --o test --regheader > identity.nofile > > arg = 6 > reading registration file 002_S/mri/aseg.mgz > regio_read_register(): Success > Error reading inplaneres from 002_S/mri/aseg.mgz > regio_read_register(): Success > Error reading inplaneres from 002_S/mri/aseg.mgz > mri_compute_volume_fractions: could not load registration file from > 002_S/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 6:21 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] mri_compute_volume_fractions > > try > > mri_compute_volume_fractions --o test --regheader > > On Wed, 25 Apr 2018, Srinivasan, Dhivya wrote: > >> 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 >> >> >> > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
