This can happen if the label is small and/or you've used a lot of smoothing. It
is better to do this kind of thing in fsaverage space rather than moving the
labels back to the individual space. If you've run mri_glmfit-sim, then it
should have created a table file (something.y.ocn.dat). This file will have a
row for each subject and a column for each cluster. The value will be the mean
for that subject in that cluster.
On 2/15/19 6:23 AM, Giuliana Klencklen wrote:
External Email - Use Caution
Hi FS experts,
I did group-level, surface-based, vertex-wise analysis for baseline and
longitudinal data. I used Qdec and do the same work with the fsgd version
(mri_glmfit-sim command) to double-check the data.
I created label files with tksurfer for each of the clusters showing a
significant between-group difference. Then, I used the following command stream
to extract the cortical thickness values for each subject and cluster:
mri_label2label, mris_anatomical_stats, and aparcstats2table.
E.g.,
mri_label2label --srcsubject fsaverage --srclabel
/home/jagust/gklenck/Long_MRI/lh.ac-baseline-rostralmiddlefrontal.label
--trgsubject ${s}_tp1 --trglabel
${s}_tp1/label/lh.ac-baseline-rostralmiddlefrontal.label --hemi lh --regmethod
surface
mris_anatomical_stats -l lh.ac-baseline-rostralmiddlefrontal.label -t
lh.thickness -b -f ${s}_tp1/stats/lh.ac-baseline-rostralmiddlefrontal.stats
${s}_tp1 lh
aparcstats2table --subjects ${s}_tp1 --hemi lh --parc
ac-baseline-rostralmiddlefrontal --meas thickness --tablefile
${out_dir}/lh.ac-baseline-rostralmiddlefrontal.aparc_stats.txt
Subsequently, when I conducted between-group comparisons for each cluster, a
couple of clusters (7 out of 16) do not show a significant difference - which
does not make sense. This problem seems to appear randomly.
Help to the FS archives, I tried to use mri_segstats command but was not able
to find a correct combination of arguments. If this is the right track to solve
this problem, what combination of arguments should I use? And if this is not,
do you have any idea how I can solve this problem?
Many thanks in advance.
Regards,
Giuliana
--
Giuliana Klencklen, Ph.D.
Helen Wills Neuroscience Institute
University of California, Berkeley
118 Barker Hall
Berkeley, CA 94720-3190
510-395-0040
giuliana.klenck...@berkeley.edu<mailto:giuliana.klenck...@berkeley.edu>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
