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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