You will need to create a segmentation volume in the subject/mri folder. For BA6, you can use lh.BA6_exvivo.thresh.label to create this volume. Use mri_label2vol. Run it with --help to get examples. You can use example #4 just with the single label above (for the output use a mgz file instead of img). When you are done, you should have a binary volume at 1mm3 with the lh BA6 -- view this to make sure it is right. Then use fcseed-config to configure this seed, specifying -segid 1 and -seg NameOfSeg.mgz
where NameOfSeg.mgz is the output of the mri_label2vol above On 11/28/2017 05:44 PM, Jessica Huang wrote: > Hi Freesurfer Experts, > > I've been looking to extract the timecourses of a couple regions of > interest from fMRI data that's be registered against anatomical data. > > I've used commands such as recon-all and preproc-sess on all subjects. > > I've already used command fcseed-sess to extract timecourses from many > regions in the default parcellations/ segmentations transferred > through previous commands. I've also used fcseed-sess for regions that > were labelled in each subject's anatomical labels folder. I'm still > curious how to extract the timecourses for other ROIs not in the > default parcellations/ segmentations. For example, with reference to > the lookup table FreeSurferColorLUT.txt, how do I access the > timecourse of: > #9 Left-Thalamus 0 118 14 0 > Thank you for any insight. Is there some folder I could look in or > specific subject files that might help? > Thank you again! > Jessica > > p.s. for more examples of timecourses I have/ don't have access to > already: > > In the default segmentation, I know how to extract these: > - 1007 ctx-lh-fusiform > > In the labels folder of each subject, I know how to extract these: > - 400 V1 > > Unsure how to extract these because they're not found in each of my > subjects: > - 406 BA6 > > -- > Harvard College Class of 2020 > A.B. Candidate in Computer Science > jessicalihuang.com <http://jessicalihuang.com> > 1 (516) 343-4850 > > > _______________________________________________ > 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.
