Hi Bruce, The aseg.mgz may be precisely what I was looking for. Good to know.
Other regions of interest include the following for our project: 17 Left-Hippocampus 220 216 20 0 53 Right-Hippocampus 220 216 20 0 415 AIPS_AIP_l 1 225 176 0 416 AIPS_AIP_r 1 225 176 0 417 AIPS_VIP_l 200 2 100 0 418 AIPS_VIP_r 200 2 100 0 419 IPL_PFcm_l 5 200 90 0 420 IPL_PFcm_r 5 200 90 0 421 IPL_PF_l 100 5 200 0 422 IPL_PFm_l 25 255 100 0 423 IPL_PFm_r 25 255 100 0 424 IPL_PFop_l 230 7 100 0 425 IPL_PFop_r 230 7 100 0 426 IPL_PF_r 100 5 200 0 427 IPL_PFt_l 150 10 200 0 428 IPL_PFt_r 150 10 200 0 429 IPL_PGa_l 175 10 176 0 430 IPL_PGa_r 175 10 176 0 431 IPL_PGp_l 10 100 255 0 432 IPL_PGp_r 10 100 255 0 433 Visual_V3d_l 150 45 70 0 434 Visual_V3d_r 150 45 70 0 435 Visual_V4_l 45 200 15 0 436 Visual_V4_r 45 200 15 0 437 Visual_V5_b 227 45 100 0 438 Visual_VP_l 227 45 100 0 439 Visual_VP_r 227 45 100 0 >From my understanding, these regions aren't in any default segmentation, so it would be a luxury to have them but I understand if this is impossible: 8001 Thalamus-Anterior 74 130 181 0 8002 Thalamus-Ventral-anterior 242 241 240 0 8003 Thalamus-Lateral-dorsal 206 65 78 0 8004 Thalamus-Lateral-posterior 120 21 133 0 8005 Thalamus-Ventral-lateral 195 61 246 0 8006 Thalamus-Ventral-posterior-medial 3 147 6 0 8007 Thalamus-Ventral-posterior-lateral 220 251 163 0 8008 Thalamus-intralaminar 232 146 33 0 8009 Thalamus-centromedian 4 114 14 0 8010 Thalamus-mediodorsal 121 184 220 0 8011 Thalamus-medial 235 11 175 0 8012 Thalamus-pulvinar 12 46 250 0 8013 Thalamus-lateral-geniculate 203 182 143 0 8014 Thalamus-medial-geniculate 42 204 167 0 Thank you Bruce! Best, Jessica On Wed, Nov 29, 2017 at 11:39 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Jessica > > it depends which ones you mean. Thalamus we label in the aseg.mgz, > although for some reason the CMA called it "thalamus proper" so that is the > index you should use (10 instead of 9 for left). What other labels do you > mean? > > Bruce > > > On Wed, 29 Nov 2017, Jessica Huang wrote: > > 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. 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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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