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
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