Re: [Freesurfer] extracting fMRI timecourses that are in FreeSurferColorLUT.txt but aren't in the automatically transferred parcellation/ segmentation

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

Re: [Freesurfer] extracting fMRI timecourses that are in FreeSurferColorLUT.txt but aren't in the automatically transferred parcellation/ segmentation

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

Re: [Freesurfer] extracting fMRI timecourses that are in FreeSurferColorLUT.txt but aren't in the automatically transferred parcellation/ segmentation

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

Re: [Freesurfer] extracting fMRI timecourses that are in FreeSurferColorLUT.txt but aren't in the automatically transferred parcellation/ segmentation

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

Re: [Freesurfer] extracting fMRI timecourses that are in FreeSurferColorLUT.txt but aren't in the automatically transferred parcellation/ segmentation

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

Re: [Freesurfer] extracting fMRI timecourses that are in FreeSurferColorLUT.txt but aren't in the automatically transferred parcellation/ segmentation

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