External Email - Use Caution Yep , I am using "o" .
I am running it on Ubuntu 16.04 and my freesurfer version is , freesurfer/5.3.0/bin/freesurfer mri_compute_volume_fractions --o test --regheader 002_S 002_S/mri/norm.mgz still I am getting , unknown option --o Trying to give as per documentation, which is --o outstem --regheader subject I am really sorry to bother you with so many questions. Is it something to do with version of freesurfer? ________________________________________ 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 11:13 AM To: Freesurfer support list Subject: Re: [Freesurfer] mri_compute_volume_fractions hmmm, are you sure you are using an "o" and not a "0"? And the --regheader syntax different than I thought, it requires two argments, a subject name and a template volume (if you are using the anatomical space, any of the conformed volumes such as the norm.mgz should be fine). For example, I run: mri_compute_volume_fractions --o test --regheader bruce.dev bruce.dev/mri/norm.mgz $Id: mri_compute_volume_fractions.c,v 1.22 2015/09/14 12:25:01 fischl Exp $ sysname Linux hostname sulc.nmr.mgh.harvard.edu machine x86_64 user fischl setenv SUBJECTS_DIR /homes/4/fischl/links/subjects cd /autofs/space/tiamat_003/users/subjects mri_compute_volume_fractions --o test --regheader bruce.dev bruce.dev/mri/norm.mgz outstem test regfile (null) regtype 0 segfile aseg.mgz . . . On Thu, 26 Apr 2018, Srinivasan, Dhivya wrote: > 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 > > > _______________________________________________ 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
