Re: [Freesurfer] Freesurfer surface circle of pre-defined size
hi sarah, you'll get a much quicker response posting PySurfer related questions to: nipy-de...@neuroimaging.scipy.org cheers, satra On Fri, Jul 26, 2013 at 12:57 PM, wrote: > Hello Freesurfer Experts, > > We would like to use PySurfer's function plot_label_foci.py to > automatically create circular labels of a pre-defined radius (eg. 14mm) on > the fsaverage surface of freesurfer. > > What are the specified units of "n_steps" in the command line argument > "utils.coord_to_label(subject_id, coord, label='coord', hemi='lh', > n_steps=50"? > > Thank you, > Sarah > ___ > 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] Freesurfer surface circle of pre-defined size
Hello Freesurfer Experts, We would like to use PySurfer's function plot_label_foci.py to automatically create circular labels of a pre-defined radius (eg. 14mm) on the fsaverage surface of freesurfer. What are the specified units of "n_steps" in the command line argument "utils.coord_to_label(subject_id, coord, label='coord', hemi='lh', n_steps=50"? Thank you, Sarah ___ 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] Freesurfer surface circle of pre-defined size
Hi Sarah, I can image several ways to do this. If you can go onto the surface and find an index that you want to be the center, then you can create a label file with a single point. It would look something like this (see fsaverage/label/lh.cortex.label for example): --cut-- #!ascii label , from subject vox2ras=TkReg 1 1 -27.106 -80.730 11.969 0.00 --cut-- In this case, the only thing that matters is the vertex number (1). Replace 1 with your vertex number. Assuming this file is called lh.point.label, run mri_label2label --srclabel lh.point.label --dilate 20 --s yoursubject --hemi lh --trglabel ./lh.point20.label --regmethod surface This will create a new label that has been dilated 20 times. You can load it in tksurfer. Is this what you want to do? doug On 07/11/2013 02:55 PM, sar...@nmr.mgh.harvard.edu wrote: > I'd like to make a circle of a pre-defined size on the freesurfer surface, > with RAS coordinates as the center of the circle. What would be the best > way to do this? > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Freesurfer surface circle of pre-defined size
I'd like to make a circle of a pre-defined size on the freesurfer surface, with RAS coordinates as the center of the circle. What would be the best way to do this? ___ 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.
