Hello,
I am interested in creating my own atlas for elderly patients with enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas?
Thanks, Brianna
Hi Brianna
what kind of atlas do you mean? If one for creating the aseg you will need to have labeled volumes for creating a new atlas
cheers Bruce
On Fri, 11 Jul 2014, Brianna Damadian wrote:
Hello,
I am interested in creating my own atlas for elderly patients with enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas?
Thanks, Brianna _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce, Would be interested in an atlas for aseg that gives total gray matter and ventricle volume. Would I be able to create an atlas based on these 30 patients with labeled volumes for just these measures? Additionally, my understanding of creating an atlas is very rudimentary - would I begin the process by running recon-all on these 30 scans and then manually editing the segmentations using tksurfer?
Thanks again, Brianna
On Fri, Jul 11, 2014 at 10:14 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Brianna
what kind of atlas do you mean? If one for creating the aseg you will need to have labeled volumes for creating a new atlas
cheers Bruce
On Fri, 11 Jul 2014, Brianna Damadian wrote:
Hello,
I am interested in creating my own atlas for elderly patients with
enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas?
Thanks, Brianna _______________________________________________ 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.
Hi Brianna
yes, that would work (although you would use freeview or tkmedit).
Why do you feel you need a new atlas? Our latest version does quite well, even on subjects with very very large ventricles. What version are you running?
cheers Bruce
On Fri, 11 Jul 2014, Brianna Damadian wrote:
Hi Bruce, Would be interested in an atlas for aseg that gives total gray matter and ventricle volume. Would I be able to create an atlas based on these 30 patients with labeled volumes for just these measures? Additionally, my understanding of creating an atlas is very rudimentary - would I begin the process by running recon-all on these 30 scans and then manually editing the segmentations using tksurfer?
Thanks again, Brianna
On Fri, Jul 11, 2014 at 10:14 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Brianna
what kind of atlas do you mean? If one for creating the aseg you will need to have labeled volumes for creating a new atlas cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: > Hello, > > I am interested in creating my own atlas for elderly patients with enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas? > > Thanks, > Brianna > _______________________________________________ > 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.
Hi Bruce, I'm using v5.3.0. Does this version do well with patients with large ventricles? Two cases I ran seemed to do well with the ventricles, but some others seem to be running into some errors (which I haven't had the time to work out yet). So in your opinion, to get our desired measures of total gray matter and ventricular volume, we would not need to create our own atlas?
Side question: Is there any literature on/do you happen to know what the margin of error for a measure like total gray matter (taken from the aseg.stats header) is in Freesurfer?
Thanks, Brianna
On Fri, Jul 11, 2014 at 10:34 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Brianna
yes, that would work (although you would use freeview or tkmedit).
Why do you feel you need a new atlas? Our latest version does quite well, even on subjects with very very large ventricles. What version are you running?
cheers Bruce
On Fri, 11 Jul 2014, Brianna Damadian wrote:
Hi Bruce, Would be interested in an atlas for aseg that gives total gray
matter and ventricle volume. Would I be able to create an atlas based on these 30 patients with labeled volumes for just these measures? Additionally, my understanding of creating an atlas is very rudimentary - would I begin the process by running recon-all on these 30 scans and then manually editing the segmentations using tksurfer?
Thanks again, Brianna
On Fri, Jul 11, 2014 at 10:14 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Brianna
what kind of atlas do you mean? If one for creating the aseg youwill need to have labeled volumes for creating a new atlas
cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: > Hello, > > I am interested in creating my own atlas for elderly patientswith enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas? > > Thanks, > Brianna > _______________________________________________ > 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 towhom 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
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.
Hi Brianna if you upload a subject that is not doing well I'll take a look. Have you tried the -bigventricles flag? cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote:
Hi Bruce, I'm using v5.3.0. Does this version do well with patients with large ventricles? Two cases I ran seemed to do well with the ventricles, but some others seem to be running into some errors (which I haven't had the time to work out yet). So in your opinion, to get our desired measures of total gray matter and ventricular volume, we would not need to create our own atlas?
Side question: Is there any literature on/do you happen to know what the margin of error for a measure like total gray matter (taken from the aseg.stats header) is in Freesurfer?
Thanks, Brianna
On Fri, Jul 11, 2014 at 10:34 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Brianna
yes, that would work (although you would use freeview or tkmedit). Why do you feel you need a new atlas? Our latest version does quite well, even on subjects with very very large ventricles. What version are you running? cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: Hi Bruce, Would be interested in an atlas for aseg that gives total gray matter and ventricle volume. Would I be able to create an atlas based on these 30 patients with labeled volumes for just these measures? Additionally, my understanding of creating an atlas is very rudimentary - would I begin the process by running recon-all on these 30 scans and then manually editing the segmentations using tksurfer? Thanks again, Brianna On Fri, Jul 11, 2014 at 10:14 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Brianna what kind of atlas do you mean? If one for creating the aseg you will need to have labeled volumes for creating a new atlas cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: > Hello, > > I am interested in creating my own atlas for elderly patients with enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas? > > Thanks, > Brianna > _______________________________________________ > 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 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.
I have not tried that yet - when would I enter this flag? During the initial recon-all coding or later? Thanks, Brianna
On Fri, Jul 11, 2014 at 10:49 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Brianna if you upload a subject that is not doing well I'll take a look. Have you tried the -bigventricles flag? cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote:
Hi Bruce, I'm using v5.3.0. Does this version do well with patients with
large ventricles? Two cases I ran seemed to do well with the ventricles, but some others seem to be running into some errors (which I haven't had the time to work out yet). So in your opinion, to get our desired measures of total gray matter and ventricular volume, we would not need to create our own atlas?
Side question: Is there any literature on/do you happen to know what the margin of error for a measure like total gray matter (taken from the aseg.stats header) is in Freesurfer?
Thanks, Brianna
On Fri, Jul 11, 2014 at 10:34 AM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Hi Brianna
yes, that would work (although you would use freeview or tkmedit). Why do you feel you need a new atlas? Our latest version does quitewell, even on subjects with very very large ventricles. What version are you running?
cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: Hi Bruce, Would be interested in an atlas for aseg that givestotal gray matter and ventricle volume. Would I be able to create an atlas based on these 30 patients with labeled volumes for just these measures? Additionally, my understanding of creating an atlas is very rudimentary - would I begin the process by running recon-all on these 30 scans and then manually editing the segmentations using tksurfer?
Thanks again, Brianna On Fri, Jul 11, 2014 at 10:14 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Brianna
what kind of atlas do you mean? If one for creating theaseg you will need to have labeled volumes for creating a new atlas
cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: > Hello, > > I am interested in creating my own atlas for elderlypatients with enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas? > > Thanks, > Brianna > _______________________________________________ > 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 theperson 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 The information in this e-mail is intended only for the person towhom 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
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.
it's a flag to recon-all. Run recon-all -help and you should find it On Fri, 11 Jul 2014, Brianna Damadian wrote:
I have not tried that yet - when would I enter this flag? During the initial recon-all coding or later? Thanks, Brianna
On Fri, Jul 11, 2014 at 10:49 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Brianna if you upload a subject that is not doing well I'll take a look. Have you tried the -bigventricles flag? cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote:
Hi Bruce, I'm using v5.3.0. Does this version do well with patients with large ventricles? Two cases I ran seemed to do well with the ventricles, but some others seem to be running into some errors (which I haven't had the time to work out yet). So in your opinion, to get our desired measures of total gray matter and ventricular volume, we would not need to create our own atlas? Side question: Is there any literature on/do you happen to know what the margin of error for a measure like total gray matter (taken from the aseg.stats header) is in Freesurfer? Thanks, Brianna On Fri, Jul 11, 2014 at 10:34 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Brianna yes, that would work (although you would use freeview or tkmedit). Why do you feel you need a new atlas? Our latest version does quite well, even on subjects with very very large ventricles. What version are you running? cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: Hi Bruce, Would be interested in an atlas for aseg that gives total gray matter and ventricle volume. Would I be able to create an atlas based on these 30 patients with labeled volumes for just these measures? Additionally, my understanding of creating an atlas is very rudimentary - would I begin the process by running recon-all on these 30 scans and then manually editing the segmentations using tksurfer? Thanks again, Brianna On Fri, Jul 11, 2014 at 10:14 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Brianna what kind of atlas do you mean? If one for creating the aseg you will need to have labeled volumes for creating a new atlas cheers Bruce On Fri, 11 Jul 2014, Brianna Damadian wrote: > Hello, > > I am interested in creating my own atlas for elderly patients with enlarged ventricles. We have about 30 patients with axial MPR scans. Is this enough to build an atlas? > > Thanks, > Brianna > _______________________________________________ > 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 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 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@nmr.mgh.harvard.edu
-
Brianna Damadian -
Bruce Fischl