Re: [Freesurfer] creating a skull
no, that should be fine On Tue, 4 Sep 2012, Borzello, Mia wrote: > I'm using Unix. Should I try something else? > > Thanks, > m > > From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] > Sent: Monday, September 03, 2012 2:45 PM > To: Borzello, Mia > Cc: freesurfer > Subject: Re: [Freesurfer] creating a skull > > Hi Mia > > what platform are you running on? > > Bruce > On Fri, 31 Aug 2012, Borzello, Mia wrote: > >> I've been referred to the following link on the freesurfer site to handle >> this, but is this still current (i.e. is linux still needed to do this?): >> http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html >> >> thanks, >> m >> >> From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu] >> Sent: Friday, August 31, 2012 10:29 AM >> To: Borzello, Mia >> Cc: freesurfer >> Subject: Re: [Freesurfer] creating a skull >> >> Hi, >> You need to add an extension onto the file name, something like brain.mgz >> or brain.nii. The extension will tell it what format to save the output >> in. >> -Louis >> >> On Fri, 31 Aug 2012, Borzello, Mia wrote: >> >>> Hi freesurfer family, >>> >>> I am trying to create the inner skull boundary and ran: mri_watershed >>> -atlas - surf -useSRAS mri.nii brain >>> >>> However, after it finished running it said it was saving "brain", but >>> "brain" was an unknown file type. Am i supposed to specify that somewhere? >>> >>> Thanks in advance, >>> m >>> >>> ___ >>> 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 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.
Re: [Freesurfer] creating a skull
I'm using Unix. Should I try something else? Thanks, m From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Monday, September 03, 2012 2:45 PM To: Borzello, Mia Cc: freesurfer Subject: Re: [Freesurfer] creating a skull Hi Mia what platform are you running on? Bruce On Fri, 31 Aug 2012, Borzello, Mia wrote: > I've been referred to the following link on the freesurfer site to handle > this, but is this still current (i.e. is linux still needed to do this?): > http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html > > thanks, > m > > From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu] > Sent: Friday, August 31, 2012 10:29 AM > To: Borzello, Mia > Cc: freesurfer > Subject: Re: [Freesurfer] creating a skull > > Hi, > You need to add an extension onto the file name, something like brain.mgz > or brain.nii. The extension will tell it what format to save the output > in. > -Louis > > On Fri, 31 Aug 2012, Borzello, Mia wrote: > >> Hi freesurfer family, >> >> I am trying to create the inner skull boundary and ran: mri_watershed -atlas >> - surf -useSRAS mri.nii brain >> >> However, after it finished running it said it was saving "brain", but >> "brain" was an unknown file type. Am i supposed to specify that somewhere? >> >> Thanks in advance, >> m >> >> ___ >> 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 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.
Re: [Freesurfer] creating a skull
Hi Mia what platform are you running on? Bruce On Fri, 31 Aug 2012, Borzello, Mia wrote: > I've been referred to the following link on the freesurfer site to handle > this, but is this still current (i.e. is linux still needed to do this?): > http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html > > thanks, > m > > From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu] > Sent: Friday, August 31, 2012 10:29 AM > To: Borzello, Mia > Cc: freesurfer > Subject: Re: [Freesurfer] creating a skull > > Hi, > You need to add an extension onto the file name, something like brain.mgz > or brain.nii. The extension will tell it what format to save the output > in. > -Louis > > On Fri, 31 Aug 2012, Borzello, Mia wrote: > >> Hi freesurfer family, >> >> I am trying to create the inner skull boundary and ran: mri_watershed -atlas >> - surf -useSRAS mri.nii brain >> >> However, after it finished running it said it was saving "brain", but >> "brain" was an unknown file type. Am i supposed to specify that somewhere? >> >> Thanks in advance, >> m >> >> ___ >> 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 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.
Re: [Freesurfer] creating a skull
did you try using freeview? For example: freeview -v brain.mgz On Fri, 31 Aug 2012, Borzello, Mia wrote: > Hi, > > I make it an mgz. When trying to load (tried using a load and read command) > to make sure it looks okay, but it's not working. How can I view this mgz > file or ascertain that it has an error? > > Thanks, > m > > From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu] > Sent: Friday, August 31, 2012 10:29 AM > To: Borzello, Mia > Cc: freesurfer > Subject: Re: [Freesurfer] creating a skull > > Hi, > You need to add an extension onto the file name, something like brain.mgz > or brain.nii. The extension will tell it what format to save the output > in. > -Louis > > On Fri, 31 Aug 2012, Borzello, Mia wrote: > >> Hi freesurfer family, >> >> I am trying to create the inner skull boundary and ran: mri_watershed -atlas >> - surf -useSRAS mri.nii brain >> >> However, after it finished running it said it was saving "brain", but >> "brain" was an unknown file type. Am i supposed to specify that somewhere? >> >> Thanks in advance, >> m >> >> ___ >> 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 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.
Re: [Freesurfer] creating a skull
Hi Mia you would need to mess around with watershed and such, it might work or might not. cheers Bruce On Mon, 3 Sep 2012, Borzello, Mia wrote: > Also, is there a way to create a skull from a CT scan? > > From: Borzello, Mia > Sent: Friday, August 31, 2012 12:17 PM > To: freesurfer > Subject: RE: [Freesurfer] creating a skull > > I've been referred to the following link on the freesurfer site to handle > this, but is this still current (i.e. is linux still needed to do this?): > http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html > > thanks, > m > > From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu] > Sent: Friday, August 31, 2012 10:29 AM > To: Borzello, Mia > Cc: freesurfer > Subject: Re: [Freesurfer] creating a skull > > Hi, > You need to add an extension onto the file name, something like brain.mgz > or brain.nii. The extension will tell it what format to save the output > in. > -Louis > > On Fri, 31 Aug 2012, Borzello, Mia wrote: > >> Hi freesurfer family, >> >> I am trying to create the inner skull boundary and ran: mri_watershed -atlas >> - surf -useSRAS mri.nii brain >> >> However, after it finished running it said it was saving "brain", but >> "brain" was an unknown file type. Am i supposed to specify that somewhere? >> >> Thanks in advance, >> m >> >> ___ >> 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 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.
Re: [Freesurfer] creating a skull
Also, is there a way to create a skull from a CT scan? From: Borzello, Mia Sent: Friday, August 31, 2012 12:17 PM To: freesurfer Subject: RE: [Freesurfer] creating a skull I've been referred to the following link on the freesurfer site to handle this, but is this still current (i.e. is linux still needed to do this?): http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html thanks, m From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu] Sent: Friday, August 31, 2012 10:29 AM To: Borzello, Mia Cc: freesurfer Subject: Re: [Freesurfer] creating a skull Hi, You need to add an extension onto the file name, something like brain.mgz or brain.nii. The extension will tell it what format to save the output in. -Louis On Fri, 31 Aug 2012, Borzello, Mia wrote: > Hi freesurfer family, > > I am trying to create the inner skull boundary and ran: mri_watershed -atlas > - surf -useSRAS mri.nii brain > > However, after it finished running it said it was saving "brain", but "brain" > was an unknown file type. Am i supposed to specify that somewhere? > > Thanks in advance, > m > > ___ > 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.
Re: [Freesurfer] creating a skull
I've been referred to the following link on the freesurfer site to handle this, but is this still current (i.e. is linux still needed to do this?): http://mailman.science.ru.nl/pipermail/fieldtrip/2012-January/004679.html thanks, m From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu] Sent: Friday, August 31, 2012 10:29 AM To: Borzello, Mia Cc: freesurfer Subject: Re: [Freesurfer] creating a skull Hi, You need to add an extension onto the file name, something like brain.mgz or brain.nii. The extension will tell it what format to save the output in. -Louis On Fri, 31 Aug 2012, Borzello, Mia wrote: > Hi freesurfer family, > > I am trying to create the inner skull boundary and ran: mri_watershed -atlas > - surf -useSRAS mri.nii brain > > However, after it finished running it said it was saving "brain", but "brain" > was an unknown file type. Am i supposed to specify that somewhere? > > Thanks in advance, > m > > ___ > 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.
Re: [Freesurfer] creating a skull
Hi, I make it an mgz. When trying to load (tried using a load and read command) to make sure it looks okay, but it's not working. How can I view this mgz file or ascertain that it has an error? Thanks, m From: Louis Nicholas Vinke [vi...@nmr.mgh.harvard.edu] Sent: Friday, August 31, 2012 10:29 AM To: Borzello, Mia Cc: freesurfer Subject: Re: [Freesurfer] creating a skull Hi, You need to add an extension onto the file name, something like brain.mgz or brain.nii. The extension will tell it what format to save the output in. -Louis On Fri, 31 Aug 2012, Borzello, Mia wrote: > Hi freesurfer family, > > I am trying to create the inner skull boundary and ran: mri_watershed -atlas > - surf -useSRAS mri.nii brain > > However, after it finished running it said it was saving "brain", but "brain" > was an unknown file type. Am i supposed to specify that somewhere? > > Thanks in advance, > m > > ___ > 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.
Re: [Freesurfer] creating a skull
Hi, You need to add an extension onto the file name, something like brain.mgz or brain.nii. The extension will tell it what format to save the output in. -Louis On Fri, 31 Aug 2012, Borzello, Mia wrote: > Hi freesurfer family, > > I am trying to create the inner skull boundary and ran: mri_watershed -atlas > - surf -useSRAS mri.nii brain > > However, after it finished running it said it was saving "brain", but "brain" > was an unknown file type. Am i supposed to specify that somewhere? > > Thanks in advance, > m > > ___ > 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] creating a skull
Hi freesurfer family, I am trying to create the inner skull boundary and ran: mri_watershed -atlas - surf -useSRAS mri.nii brain However, after it finished running it said it was saving "brain", but "brain" was an unknown file type. Am i supposed to specify that somewhere? Thanks in advance, m ___ 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.
