Hi all,
I’m trying to extract individual cortical thickness values using the output of the annotation file from mri_glmfit-sim. This worked well for the left hemisphere, we got values that were significantly different between groups we had specified in mri_glmfit, but for the right hemisphere we get all values of 0 for the cortical thickness and mean curvature. I’ll post the commands I’m running below. Essentially I’m attempting to take the annot file from mri_glmfit-sim, convert it to a label, then put that label onto a subject (which may or may not be necessary), and pull out the anatomical stats using that label. Below is the example code for one subject. I did also confirm that the initial annot file, and the final subject label both sit on the right hemisphere when loading them up in freeview. I’ll also attach the summary file from mri_glmfit-sim for the cluster and a sample recon-all log.
Any help is appreciated!
- Taylor H. Lab Data Coordinator LRDC, University of Pittsburgh
mri_annotation2label --subject fsaverage --hemi rh --outdir ./scripts --annotation archive/rh.PYS_Can3_2.glmdir/PYS_Can3_2/cache.th40.neg.sig.ocn.annot --label 1
mri_label2label --srcsubject fsaverage --srclabel scripts/rh.cluster-001.label --trglabel s72064/label/rh.cluster-001.label --trgsubject s72064 --hemi rh --regmethod surface
mris_anatomical_stats -l s72064/label/rh.cluster-001.label -b s72064 rh >> s72064/scripts/rh-cluster001.txt
Using TH3 vertex volume calc Total face volume 228346 Total vertex volume 224557 (mask=0)
table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name
86 64 179 0.000 0.000 0.108 0.018 1 0.1 s72064/label/rh.cluster-001.label