They do not have any normalization applied. BTW, you should not scale the thickness by the ICV

On 3/18/19 10:24 AM, Bunting, Emma wrote:

External Email - Use Caution Hi Freesurfer experts,

I used a script created by ENIGMA to extract the cortical thickness values for 129 subjects that had undergone reconall processing.

We are using these values in VBM analysis. From reading other papers, we notice that all regional volumes are usually normalised by dividing by total intracranial volumes for each subject.

I’m just wondering whether the values we are extracting from our freesurfer output files have already had this normalisation applied?

The script we’ve used as follows:

#!/bin/bash

echo 'SubjID,L_bankssts_thickavg,L_caudalanteriorcingulate_thickavg,L_caudalmiddlefrontal_thickavg,L_cuneus_thickavg,L_entorhinal_thickavg,L_fusiform_thickavg,L_inferiorparietal_thickavg,L_inferiortemporal_thickavg,L_isthmuscingulate_thickavg,L_lateraloccipital_thickavg,L_lateralorbitofrontal_thickavg,L_lingual_thickavg,L_medialorbitofrontal_thickavg,L_middletemporal_thickavg,L_parahippocampal_thickavg,L_paracentral_thickavg,L_parsopercularis_thickavg,L_parsorbitalis_thickavg,L_parstriangularis_thickavg,L_pericalcarine_thickavg,L_postcentral_thickavg,L_posteriorcingulate_thickavg,L_precentral_thickavg,L_precuneus_thickavg,L_rostralanteriorcingulate_thickavg,L_rostralmiddlefrontal_thickavg,L_superiorfrontal_thickavg,L_superiorparietal_thickavg,L_superiortemporal_thickavg,L_supramarginal_thickavg,L_frontalpole_thickavg,L_temporalpole_thickavg,L_transversetemporal_thickavg,L_insula_thickavg,R_bankssts_thickavg,R_caudalanteriorcingulate_thickavg,R_caudalmiddlefrontal_thickavg,R_cuneus_thickavg,R_entorhinal_thickavg,R_fusiform_thickavg,R_inferiorparietal_thickavg,R_inferiortemporal_thickavg,R_isthmuscingulate_thickavg,R_lateraloccipital_thickavg,R_lateralorbitofrontal_thickavg,R_lingual_thickavg,R_medialorbitofrontal_thickavg,R_middletemporal_thickavg,R_parahippocampal_thickavg,R_paracentral_thickavg,R_parsopercularis_thickavg,R_parsorbitalis_thickavg,R_parstriangularis_thickavg,R_pericalcarine_thickavg,R_postcentral_thickavg,R_posteriorcingulate_thickavg,R_precentral_thickavg,R_precuneus_thickavg,R_rostralanteriorcingulate_thickavg,R_rostralmiddlefrontal_thickavg,R_superiorfrontal_thickavg,R_superiorparietal_thickavg,R_superiortemporal_thickavg,R_supramarginal_thickavg,R_frontalpole_thickavg,R_temporalpole_thickavg,R_transversetemporal_thickavg,R_insula_thickavg,LThickness,RThickness,LSurfArea,RSurfArea,ICV' > CorticalMeasuresENIGMA_ThickAvg.csv echo 'SubjID,L_bankssts_surfavg,L_caudalanteriorcingulate_surfavg,L_caudalmiddlefrontal_surfavg,L_cuneus_surfavg,L_entorhinal_surfavg,L_fusiform_surfavg,L_inferiorparietal_surfavg,L_inferiortemporal_surfavg,L_isthmuscingulate_surfavg,L_lateraloccipital_surfavg,L_lateralorbitofrontal_surfavg,L_lingual_surfavg,L_medialorbitofrontal_surfavg,L_middletemporal_surfavg,L_parahippocampal_surfavg,L_paracentral_surfavg,L_parsopercularis_surfavg,L_parsorbitalis_surfavg,L_parstriangularis_surfavg,L_pericalcarine_surfavg,L_postcentral_surfavg,L_posteriorcingulate_surfavg,L_precentral_surfavg,L_precuneus_surfavg,L_rostralanteriorcingulate_surfavg,L_rostralmiddlefrontal_surfavg,L_superiorfrontal_surfavg,L_superiorparietal_surfavg,L_superiortemporal_surfavg,L_supramarginal_surfavg,L_frontalpole_surfavg,L_temporalpole_surfavg,L_transversetemporal_surfavg,L_insula_surfavg,R_bankssts_surfavg,R_caudalanteriorcingulate_surfavg,R_caudalmiddlefrontal_surfavg,R_cuneus_surfavg,R_entorhinal_surfavg,R_fusiform_surfavg,R_inferiorparietal_surfavg,R_inferiortemporal_surfavg,R_isthmuscingulate_surfavg,R_lateraloccipital_surfavg,R_lateralorbitofrontal_surfavg,R_lingual_surfavg,R_medialorbitofrontal_surfavg,R_middletemporal_surfavg,R_parahippocampal_surfavg,R_paracentral_surfavg,R_parsopercularis_surfavg,R_parsorbitalis_surfavg,R_parstriangularis_surfavg,R_pericalcarine_surfavg,R_postcentral_surfavg,R_posteriorcingulate_surfavg,R_precentral_surfavg,R_precuneus_surfavg,R_rostralanteriorcingulate_surfavg,R_rostralmiddlefrontal_surfavg,R_superiorfrontal_surfavg,R_superiorparietal_surfavg,R_superiortemporal_surfavg,R_supramarginal_surfavg,R_frontalpole_surfavg,R_temporalpole_surfavg,R_transversetemporal_surfavg,R_insula_surfavg,LThickness,RThickness,LSurfArea,RSurfArea,ICV' > CorticalMeasuresENIGMA_SurfAvg.csv

for subj_id in $(ls -d Subj*); do #may need to change this so that it selects subjects with FS output

printf "%s," "${subj_id}" >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%s," "${subj_id}" >> CorticalMeasuresENIGMA_SurfAvg.csv

for side in lh.aparc.stats rh.aparc.stats; do

for x in bankssts caudalanteriorcingulate caudalmiddlefrontal cuneus entorhinal fusiform inferiorparietal inferiortemporal isthmuscingulate lateraloccipital lateralorbitofrontal lingual medialorbitofrontal middletemporal parahippocampal paracentral parsopercularis parsorbitalis parstriangularis pericalcarine postcentral posteriorcingulate precentral precuneus rostralanteriorcingulate rostralmiddlefrontal superiorfrontal superiorparietal superiortemporal supramarginal frontalpole temporalpole transversetemporal insula; do

printf "%g," `grep -w ${x} ${subj_id}/stats/${side} | awk '{print $5}'` >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%g," `grep -w ${x} ${subj_id}/stats/${side} | awk '{print $3}'` >> CorticalMeasuresENIGMA_SurfAvg.csv

done done

printf "%g," `cat ${subj_id}/stats/lh.aparc.stats | grep MeanThickness | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%g," `cat ${subj_id}/stats/rh.aparc.stats | grep MeanThickness | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%g," `cat ${subj_id}/stats/lh.aparc.stats | grep MeanThickness | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_SurfAvg.csv printf "%g," `cat ${subj_id}/stats/rh.aparc.stats | grep MeanThickness | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_SurfAvg.csv printf "%g," `cat ${subj_id}/stats/lh.aparc.stats | grep WhiteSurfArea | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%g," `cat ${subj_id}/stats/rh.aparc.stats | grep WhiteSurfArea | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%g," `cat ${subj_id}/stats/lh.aparc.stats | grep WhiteSurfArea | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_SurfAvg.csv printf "%g," `cat ${subj_id}/stats/rh.aparc.stats | grep WhiteSurfArea | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_SurfAvg.csv printf "%g" `cat ${subj_id}/stats/aseg.stats | grep IntraCranialVol | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_ThickAvg.csv printf "%g" `cat ${subj_id}/stats/aseg.stats | grep IntraCranialVol | awk -F, '{print $4}'` >> CorticalMeasuresENIGMA_SurfAvg.csv

echo "" >> CorticalMeasuresENIGMA_ThickAvg.csv echo "" >> CorticalMeasuresENIGMA_SurfAvg.csv

done

Please let me know if you need any other info,

Best wishes,

Emma

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