If all you want is the mean time course from hippocampus, there is an easier/better way, eg

First, create a configuration that describes the ROI you want, eg,
fcseed-config -segid 17 -fcname L_Hippo.dat -fsd bold -mean -cfg mean.L_Hippo.config
This is done once regardless of how many subjects you have
Then for each subject, run
fcseed-sess  -s sessionid -cfg L_Hippo.config
This will create L_Hippo.dat in each run folder
Note that "17" comes from $FREESURFER_HOME/FreeSurferColorLUT.txt



On 6/1/2022 1:41 PM, Mingyang Xia wrote:

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Dear freesurfer expert:
  I use freesurfer to preprocess the fmri signal. It generates three final files: fmcpr.up.sm5.fsaverage.lh.nii.gz, fmcpr.up.sm5.fsaverage.rh.nii.gz, and fmcpr.up.sm5.mni305.2. However I want to extract the subcortical area signal, for example the signal on the hippocampus. How could I extract the signal in the subcortical areas and find their labels and corresponding files?
  Thank you
  Mingyang

On Tue, May 31, 2022 at 8:16 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
what do you man by the label of the file? If  you want a mask, there should be a mask in the mask folder

On 5/23/2022 10:05 PM, Mingyang Xia wrote:

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Dear Freesurfer expert:
  I am Mingyang Xia. I use freesurfer to preprocess the fmri data and map to the fsaverage and generate a file named fmcpr.up.sm5.mni305.2mm.nii.gz. I want to get the label of this file however I could not find the label in the fsaverage folder. Could you give me some advice?
  Thank you
  Mingyang Xia

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