Dear FS experts We used mris_make_face_parcellation to get a finer parcellation of the cortical surface. The labels of the resulting parcellations are consecutively numbered, but there is no information about the anatomical location of these parcellations.
In a first step, we would like to know which of the new parcellations are located within a particular brain structure (label), e.g. within the central sulcus as defined in the aparc.a2009s.annot.
In a second step, we would like to extract the MNI coordinates of the centroids of these new parcellations.
All suggestions are appreciated.
Thanks in advance Best regards
Diana
Hi Diana,
the parcels from mris_make_face_parcellation are uniform, not localized to gyral/sulcal labels. If that is important try using mris_divide_parcellation instead.
cheers Bruce
On Sun, 11 Apr 2010, Diana Wotruba wrote:
Dear FS experts We used mris_make_face_parcellation to get a finer parcellation of the cortical surface. The labels of the resulting parcellations are consecutively numbered, but there is no information about the anatomical location of these parcellations.
In a first step, we would like to know which of the new parcellations are located within a particular brain structure (label), e.g. within the central sulcus as defined in the aparc.a2009s.annot.
In a second step, we would like to extract the MNI coordinates of the centroids of these new parcellations.
All suggestions are appreciated.
Thanks in advance Best regards
Diana _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Bruce Thank you for the quick answer. We already considered using mris_divide_parcellation. Unfortunately the result is a strip shaped parcellation scheme, which is not suitable for our aim. Therefore we would rather use mris_make_face_parcellation. Is there no other way to get the MNI Coordinates of these vertices and the label corresponding to them?
Thanks very much for your help! Kind regards Diana
Am 12.04.2010 um 00:31 schrieb Bruce Fischl:
Hi Diana,
the parcels from mris_make_face_parcellation are uniform, not localized to gyral/sulcal labels. If that is important try using mris_divide_parcellation instead.
cheers Bruce
On Sun, 11 Apr 2010, Diana Wotruba wrote:
Dear FS experts We used mris_make_face_parcellation to get a finer parcellation of the cortical surface. The labels of the resulting parcellations are consecutively numbered, but there is no information about the anatomical location of these parcellations.
In a first step, we would like to know which of the new parcellations are located within a particular brain structure (label), e.g. within the central sulcus as defined in the aparc.a2009s.annot.
In a second step, we would like to extract the MNI coordinates of the centroids of these new parcellations.
All suggestions are appreciated.
Thanks in advance Best regards
Diana _______________________________________________ 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.
yes, you can use the talairach.xfm file to get MNI coords of whatever you want. Not sure if it is reported anywhere by default though. Doug? On Wed, 14 Apr 2010, Diana Wotruba wrote:
Hi Bruce Thank you for the quick answer. We already considered using mris_divide_parcellation. Unfortunately the result is a strip shaped parcellation scheme, which is not suitable for our aim. Therefore we would rather use mris_make_face_parcellation. Is there no other way to get the MNI Coordinates of these vertices and the label corresponding to them?
Thanks very much for your help! Kind regards Diana
Am 12.04.2010 um 00:31 schrieb Bruce Fischl:
Hi Diana,
the parcels from mris_make_face_parcellation are uniform, not localized to gyral/sulcal labels. If that is important try using mris_divide_parcellation instead.
cheers Bruce
On Sun, 11 Apr 2010, Diana Wotruba wrote:
Dear FS experts We used mris_make_face_parcellation to get a finer parcellation of the cortical surface. The labels of the resulting parcellations are consecutively numbered, but there is no information about the anatomical location of these parcellations.
In a first step, we would like to know which of the new parcellations are located within a particular brain structure (label), e.g. within the central sulcus as defined in the aparc.a2009s.annot.
In a second step, we would like to extract the MNI coordinates of the centroids of these new parcellations.
All suggestions are appreciated.
Thanks in advance Best regards
Diana _______________________________________________ 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
Hi We were able to extract the vertex number (and MNI coordinates) for the finer parcellation as well as for the aparc.a2005s parcellation by using mri_annotation2label. Now we have a .label file for each parcellation where all vertices number (and their coordinates) that belong to a parcellation are listed.
Do you have any suggestion or idea how to match the vertex number for both parcellations in order to get the anatomical labels for the finer parcellation?
Kind regards Diana Am 14.04.2010 um 15:01 schrieb Bruce Fischl:
yes, you can use the talairach.xfm file to get MNI coords of whatever you want. Not sure if it is reported anywhere by default though. Doug? On Wed, 14 Apr 2010, Diana Wotruba wrote:
Hi Bruce Thank you for the quick answer. We already considered using mris_divide_parcellation. Unfortunately the result is a strip shaped parcellation scheme, which is not suitable for our aim. Therefore we would rather use mris_make_face_parcellation. Is there no other way to get the MNI Coordinates of these vertices and the label corresponding to them?
Thanks very much for your help! Kind regards Diana
Am 12.04.2010 um 00:31 schrieb Bruce Fischl:
Hi Diana,
the parcels from mris_make_face_parcellation are uniform, not localized to gyral/sulcal labels. If that is important try using mris_divide_parcellation instead.
cheers Bruce
On Sun, 11 Apr 2010, Diana Wotruba wrote:
Dear FS experts We used mris_make_face_parcellation to get a finer parcellation of the cortical surface. The labels of the resulting parcellations are consecutively numbered, but there is no information about the anatomical location of these parcellations.
In a first step, we would like to know which of the new parcellations are located within a particular brain structure (label), e.g. within the central sulcus as defined in the aparc.a2009s.annot.
In a second step, we would like to extract the MNI coordinates of the centroids of these new parcellations.
All suggestions are appreciated.
Thanks in advance Best regards
Diana _______________________________________________ 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
Hi Diana,
the vertex # should be the same in all parcellation, so you just need to lookup a different label for the same index. Note that you can load the annotations into matlab using read_annotation.m if you want.
cheers, Bruce On Thu, 15 Apr 2010, Diana Wotruba wrote:
Hi We were able to extract the vertex number (and MNI coordinates) for the finer parcellation as well as for the aparc.a2005s parcellation by using mri_annotation2label. Now we have a .label file for each parcellation where all vertices number (and their coordinates) that belong to a parcellation are listed.
Do you have any suggestion or idea how to match the vertex number for both parcellations in order to get the anatomical labels for the finer parcellation?
Kind regards Diana Am 14.04.2010 um 15:01 schrieb Bruce Fischl:
yes, you can use the talairach.xfm file to get MNI coords of whatever you want. Not sure if it is reported anywhere by default though. Doug? On Wed, 14 Apr 2010, Diana Wotruba wrote:
Hi Bruce Thank you for the quick answer. We already considered using mris_divide_parcellation. Unfortunately the result is a strip shaped parcellation scheme, which is not suitable for our aim. Therefore we would rather use mris_make_face_parcellation. Is there no other way to get the MNI Coordinates of these vertices and the label corresponding to them?
Thanks very much for your help! Kind regards Diana
Am 12.04.2010 um 00:31 schrieb Bruce Fischl:
Hi Diana,
the parcels from mris_make_face_parcellation are uniform, not localized to gyral/sulcal labels. If that is important try using mris_divide_parcellation instead.
cheers Bruce
On Sun, 11 Apr 2010, Diana Wotruba wrote:
Dear FS experts We used mris_make_face_parcellation to get a finer parcellation of the cortical surface. The labels of the resulting parcellations are consecutively numbered, but there is no information about the anatomical location of these parcellations.
In a first step, we would like to know which of the new parcellations are located within a particular brain structure (label), e.g. within the central sulcus as defined in the aparc.a2009s.annot.
In a second step, we would like to extract the MNI coordinates of the centroids of these new parcellations.
All suggestions are appreciated.
Thanks in advance Best regards
Diana _______________________________________________ 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@nmr.mgh.harvard.edu
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Bruce Fischl -
Diana Wotruba