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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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