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:
- create annotation file for lobes: mri_annotation2label --subject $s
--hemi lh --lobesStrict lh.lobesStrict.annot
- extract lobe labels: mri_annotation2label --subject $s --hemi lh
--annotation lobesStrict --outdir $s/label
- 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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