I don't think you need to do steps 2 and 3. Just run mri_annotomical_stats on the lobes annot just like it is done for aparc. Look in the recon-all.log file for the command line doug On 07/08/2014 02:42 PM, krista kelly wrote:

Hi all,

I'm trying to extract cortical thickness data from each lobe per participant. Here are the commands I used so far:

1. create annotation file for lobes: mri_annotation2label --subject $s

--hemi lh --lobesStrict lh.lobesStrict.annot

2. extract lobe labels: mri_annotation2label --subject $s --hemi lh

--annotation lobesStrict --outdir $s/label

3. create stats file for each lobe per participant:

mris_anatomical_stats -a $s/label/lh.lobesStrict.annot -b -f $s/stats/lh.lobesStrict.stats

PROBLEM: I'm stuck now on how to compile all of the data into one file. I've tried:

aparcstats2table --subjects <subjectlist> --parc lobesStrict.annot --hemi lh –meas thickness --tablefile lh.lobesStrict.thickness.stats.txt

I've also tried:

asegstats2table --subjects <subjectlist> --subdir=stats --statsfile lh.lobesStrict --tablefile lh.lobesStrict.thickness.stats.txt

None of these work. Can someone please tell me what I'm doing wrong?

Thanks! Krista

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