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:
1. 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
2. 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
3. Configure my seed: fcseed-config -seg lh.xxx.mgz -segid 1 -fcname
lh.xxx.dat -fsd RESTING -mean -cfg mean.lh.xxx.config
4. 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 <dgr...@mgh.harvard.edu
<mailto:dgr...@mgh.harvard.edu>> wrote:
On 7/10/2021 12:47 AM, Erik Jahner wrote:
External Email - Use Caution
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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