Try using --fill-ribbon when running mri_label2vol
On 7/12/2021 12:26 PM, Erik Jahner wrote:
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Thank you very much for your assistance. In retrospect, my first question was a bit silly.
I do have a follow-up question.
I have a label that was made from a modified parcelation of the Yeo atlas. When I attempt to project that label onto the voxel space it only sparsely fills the cortical strip from the aseg cortical mask. For two of my participants it does not identify any voxels. If someone could let me know what I have done wrong it would be greatly appreciated. Here is the process i'm following:
- Copy my label constructed in fsaverage to the participants:
mri_label2label --srcsubject fsaverage --srclabel $FREESURFER_HOME/subjects/fsaverage/label/lh.xxx.label --trgsubject subject401 --trglabel subject401/label/lh.xxx.label --hemi lh --regmethod surface
- Convert the labels to volumes: mri_label2vol --label
subject401/label/lh.xxx.label --temp subject401/mri/orig.mgz --identity --o subject401/mri/lh.xxx.mgz --hemi lh
- Configure my seed: fcseed-config -seg lh.xxx.mgz -segid 1 -fcname
lh.xxx.dat -fsd RESTING -mean -cfg mean.lh.xxx.config
- Create the waveform: fcseed-sess -sf sessid -cfg mean.lh.xxx.config
For some participants I then get this error and it appears my label is not transforming into a volume appropriately when I examine the data. "ERROR: no voxels found in segmentation".
Thanks again for all your assistance.
~Erik Jahner
On 11 Jul 2021, at 7:52 AM, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
On 7/10/2021 12:47 AM, Erik Jahner wrote:
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I am interested in obtaining the average intensity within a label from each frame of a functional image that has been smoothed on the surface (I have generated the label). However, the functional connectivity pipeline seems to use only volume based seeds. It seems to me that in using the FreeSurfer software we would want to take advantage of the surface based smoothing and not return to getting the average of voxels in aparc+aseg.
(1) Am I incorrect in my thinking here?
Yes. If you are going to average within an ROI, there is no need to smooth. In fact, it can be counter productive as is smears one ROI into another.
(2) Is there a way to get the mean intensity of a label (I have created) at each frame along the surface to get a timcourse for a particular region?
Yes, mri_segstats. Use the --slabel option with --excludeid 0 and specify the --avgwf option for the output. Spec your surface-sampled fmri as the input --i
I see there is a way to do this with anatomical features such as thickness, but I do not see a way to do this with functional data across frames for signal intensity.
Thanks ~Erik Jahner
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