Re: [Freesurfer] Use our own training subjects?
Hi Susan - Currently the only way to read in the manually labeled streamlines from the training subjects is in .trk format, which is what trackvis writes out. If you prefer to use another program for manual labeling, then its output would have to be converted to .trk format. This format is described in the online documentation for trackvis. The priors are generated by trac-all on the fly, given the .trk files and aparc+aseg for each of the training subjects. So once the manual labeling is done, it's just about transforming these files to the template space and passing the list to trac-all. I'm happy to document this part. The hard work is the manual labeling! Hope this helps, a.y On Wed, 1 May 2013, Susan Kuo wrote: Hi Anastasia, I would like to add several tracts of interest to our priors, e.g. the IFO and sections of the corpus callosum. Would it be possible for you to document how your group created your priors? Are we constrained to trackvis as a program? I know this is a lot of documentation, but I would be happy to help. I'm located on the NIH campus, and can travel up to help with the documentation if you'd like. It would be a good learning process for me. Thank you! Susan Kuo On Fri, Apr 26, 2013 at 1:42 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - If you can label the connection that you want in trackvis consistently in a set of subjects, then yes, it'd be possible to create your own mini atlas. You'd have to map the .trk files with the trackvis streamlines and the aparc+aseg's from all the training subjects to either the MNI or the CVS template. Then there's a trainfile variable that you can set in the configuration file that tells trac-all where to find the training data. If you decide to go through with this, I can try to document it in more detail on the wiki. a.y On Mon, 15 Apr 2013, Susan Kuo wrote: Hi Anastasia, We were viewing the arcuate fasiculus tract created by TRACULA, and noticed that the tract did not reach Broca's area. While there exists literature that now challenges this neuroanatomical convention, I would like to investigate the possibility of creating and inputting on our own training subjects as priors. Do you know if we can try this? Thank you! -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear 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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear ___ 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] Use our own training subjects?
Thank you, Anastasia. I think we can recruit some hard-working neuroanatomists here to help us with the labeling. I believe I will give this a shot for the IFO. Again, thanks for your support on this - I really appreciate it! Susie Kuo On Wed, May 1, 2013 at 11:04 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susan - Currently the only way to read in the manually labeled streamlines from the training subjects is in .trk format, which is what trackvis writes out. If you prefer to use another program for manual labeling, then its output would have to be converted to .trk format. This format is described in the online documentation for trackvis. The priors are generated by trac-all on the fly, given the .trk files and aparc+aseg for each of the training subjects. So once the manual labeling is done, it's just about transforming these files to the template space and passing the list to trac-all. I'm happy to document this part. The hard work is the manual labeling! Hope this helps, a.y On Wed, 1 May 2013, Susan Kuo wrote: Hi Anastasia, I would like to add several tracts of interest to our priors, e.g. the IFO and sections of the corpus callosum. Would it be possible for you to document how your group created your priors? Are we constrained to trackvis as a program? I know this is a lot of documentation, but I would be happy to help. I'm located on the NIH campus, and can travel up to help with the documentation if you'd like. It would be a good learning process for me. Thank you! Susan Kuo On Fri, Apr 26, 2013 at 1:42 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - If you can label the connection that you want in trackvis consistently in a set of subjects, then yes, it'd be possible to create your own mini atlas. You'd have to map the .trk files with the trackvis streamlines and the aparc+aseg's from all the training subjects to either the MNI or the CVS template. Then there's a trainfile variable that you can set in the configuration file that tells trac-all where to find the training data. If you decide to go through with this, I can try to document it in more detail on the wiki. a.y On Mon, 15 Apr 2013, Susan Kuo wrote: Hi Anastasia, We were viewing the arcuate fasiculus tract created by TRACULA, and noticed that the tract did not reach Broca's area. While there exists literature that now challenges this neuroanatomical convention, I would like to investigate the possibility of creating and inputting on our own training subjects as priors. Do you know if we can try this? Thank you! -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear 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/**compliancelinehttp://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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ 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] Use our own training subjects?
Hi Anastasia, We were viewing the arcuate fasiculus tract created by TRACULA, and noticed that the tract did not reach Broca's area. While there exists literature that now challenges this neuroanatomical convention, I would like to investigate the possibility of creating and inputting on our own training subjects as priors. Do you know if we can try this? Thank you! -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ 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.
