Re: [Freesurfer] mris_divide_parcellation replication
Hi Bruce, Thanks for your reply. This makes sense. One remaining question is which surface is used to compute the eigen-axis, is it the white surface? Best, Martin On 02/03/14 15:27, Bruce Fischl wrote: Hi Christian and Martin mris_divide_parcellation finds the primary eigen-axis of the parcellation along the cortical surface, then splits it up into as many units as specified (either enough to get it under the area threshold, or explicitly specifed in a split file) cheers Bruce p.s. the code is open source so you are always welcome to grab it and take a look On Mon, 3 Feb 2014, Martin Luessi wrote: I'm wondering about this as well. It would be great if someone who is familiar with the FreeSurfer code could explain the split algorithm. Best, Martin On 01/29/14 14:36, Christian Brodbeck wrote: Dear Freesurfer developers, I am trying to replicate mris_divide_parcellation for mne-python (https://github.com/mne-tools/mne-python/pull/1085). I think I am doing the same as the MRISdivideAnnotationUnit function (https://github.com/neurodebian/freesurfer/blob/master/utils/annotation.c#L473), but the result still looks different. Could someone point out how exactly the split is done, and if there are any steps in addition to the function? Are there any measures that are taken when the split would result in two disconnected regions belonging to the same label? And what surface is the split performed on (I would assume that would be “white”)? Thank you! Christian ___ 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 -- Martin Luessi, Ph.D. Research Fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 Fax: +1 617 726-7422 ___ 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] mris_divide_parcellation replication
Thanks a lot Bruce! Using the sphere surface was what I was missing. Christian On Feb 4, 2014, at 12:16, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: it's the ?h.sphere so that folding isn't an issue On Tue, 4 Feb 2014, Martin Luessi wrote: Hi Bruce, Thanks for your reply. This makes sense. One remaining question is which surface is used to compute the eigen-axis, is it the white surface? Best, Martin On 02/03/14 15:27, Bruce Fischl wrote: Hi Christian and Martin mris_divide_parcellation finds the primary eigen-axis of the parcellation along the cortical surface, then splits it up into as many units as specified (either enough to get it under the area threshold, or explicitly specifed in a split file) cheers Bruce p.s. the code is open source so you are always welcome to grab it and take a look On Mon, 3 Feb 2014, Martin Luessi wrote: I'm wondering about this as well. It would be great if someone who is familiar with the FreeSurfer code could explain the split algorithm. Best, Martin On 01/29/14 14:36, Christian Brodbeck wrote: Dear Freesurfer developers, I am trying to replicate mris_divide_parcellation for mne-python (https://github.com/mne-tools/mne-python/pull/1085). I think I am doing the same as the MRISdivideAnnotationUnit function (https://github.com/neurodebian/freesurfer/blob/master/utils/annotation.c#L473), but the result still looks different. Could someone point out how exactly the split is done, and if there are any steps in addition to the function? Are there any measures that are taken when the split would result in two disconnected regions belonging to the same label? And what surface is the split performed on (I would assume that would be “white”)? Thank you! Christian ___ 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
Re: [Freesurfer] mris_divide_parcellation replication
Hi Christian and Martin mris_divide_parcellation finds the primary eigen-axis of the parcellation along the cortical surface, then splits it up into as many units as specified (either enough to get it under the area threshold, or explicitly specifed in a split file) cheers Bruce p.s. the code is open source so you are always welcome to grab it and take a look On Mon, 3 Feb 2014, Martin Luessi wrote: I'm wondering about this as well. It would be great if someone who is familiar with the FreeSurfer code could explain the split algorithm. Best, Martin On 01/29/14 14:36, Christian Brodbeck wrote: Dear Freesurfer developers, I am trying to replicate mris_divide_parcellation for mne-python (https://github.com/mne-tools/mne-python/pull/1085). I think I am doing the same as the MRISdivideAnnotationUnit function (https://github.com/neurodebian/freesurfer/blob/master/utils/annotation.c#L473), but the result still looks different. Could someone point out how exactly the split is done, and if there are any steps in addition to the function? Are there any measures that are taken when the split would result in two disconnected regions belonging to the same label? And what surface is the split performed on (I would assume that would be “white”)? Thank you! Christian ___ 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.
