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 fischl@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 < fischl@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 <greve@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 greve@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
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