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
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422
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--
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jessicalihuang.com
1 (516) 343-4850
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