Hi Freesurfer Experts, Can I extract time courses for regions without labels in the subject/mri folder?
Thank you for your insight! Best, Jessica On Tue, Nov 28, 2017 at 5:51 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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. > -- Harvard College Class of 2020 A.B. Candidate in Computer Science jessicalihuang.com 1 (516) 343-4850
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