Hi Bruce, Ah! I found these regions (ex. the thalamus) in the FreeSurferColorLUT.txt lookup table but otherwise not in each subject's aseg/apar/label dir. Would you have any suggestions for how to extract a timecourse for the thalamus or the hippocampus? Did I miss a step? I have labels for the following regions for all subjects:
BA1 BA2 BA3a BA3b BA4a BA4p BA6 BA44 BA45 cortex entorhinal medial wall MT perirhinal ribbon V1 V2 As a correction, I misclassified in my initial email - I do have the label for BA6. Thank you for your insight!! Best, Jessica On Wed, Nov 29, 2017 at 10:01 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Jessica > > not sure I understand, but I don't think so. If we didn't label it in the > aseg/aparc/label dir then how would you find it? Or do you mean manually > draw it? That is possible. > > Bruce > > On Wed, 29 Nov 2017, Jessica Huang wrote: > > 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 2020A.B. Candidate in Computer Science >> jessicalihuang.com >> 1 (516) 343-4850 >> >> > _______________________________________________ > 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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