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 fro
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 o
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
wrote:
> You will need to create a segmentation volume in the subject/mri folder.
> For BA6, you c
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 regi
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 fo
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
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-Hippocampus220 216 20 0
53 Right-Hippocampus 220 216 20 0
415 AIPS_AIP_l