Hi Emma
in principle of volume is proportional to ICV you would need to scale the thickness by (ICV)^(1/3). In practice we find that scaling the thickness doesn't really change the variance and loses you a DOF so we don't usually do it.
cheers Bruce
On Sat, 11 May 2019, Bunting, Emma wrote:
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Hi Doug,Why should we not scale the thickness by the ICV? This is what we had thought to be the norm based on the literature,
How would you advise normalising these values instead? Best wishes, Emma Greve, Douglas N.,Ph.D. Mon, 18 Mar 2019 07:56:18 -0700They 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:
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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_cun eus_thickavg,L_entorhinal_thickavg,L_fusiform_thickavg,L_inferiorparietal_thickavg,L_inferiortempor al_thickavg,L_isthmuscingulate_thickavg,L_lateraloccipital_thickavg,L_lateralorbitofrontal_thickavg ,L_lingual_thickavg,L_medialorbitofrontal_thickavg,L_middletemporal_thickavg,L_parahippocampal_thic kavg,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_thic kavg,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_thickav g,R_paracentral_thickavg,R_parsopercularis_thickavg,R_parsorbitalis_thickavg,R_parstriangularis_thi ckavg,R_pericalcarine_thickavg,R_postcentral_thickavg,R_posteriorcingulate_thickavg,R_precentral_th ickavg,R_precuneus_thickavg,R_rostralanteriorcingulate_thickavg,R_rostralmiddlefrontal_thickavg,R_s uperiorfrontal_thickavg,R_superiorparietal_thickavg,R_superiortemporal_thickavg,R_supramarginal_thi ckavg,R_frontalpole_thickavg,R_temporalpole_thickavg,R_transversetemporal_thickavg,R_insula_thickav g,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_surf avg,L_isthmuscingulate_surfavg,L_lateraloccipital_surfavg,L_lateralorbitofrontal_surfavg,L_lingual_ surfavg,L_medialorbitofrontal_surfavg,L_middletemporal_surfavg,L_parahippocampal_surfavg,L_paracent ral_surfavg,L_parsopercularis_surfavg,L_parsorbitalis_surfavg,L_parstriangularis_surfavg,L_pericalc arine_surfavg,L_postcentral_surfavg,L_posteriorcingulate_surfavg,L_precentral_surfavg,L_precuneus_s urfavg,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_caudalan teriorcingulate_surfavg,R_caudalmiddlefrontal_surfavg,R_cuneus_surfavg,R_entorhinal_surfavg,R_fusif orm_surfavg,R_inferiorparietal_surfavg,R_inferiortemporal_surfavg,R_isthmuscingulate_surfavg,R_late raloccipital_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_sur favg,R_rostralmiddlefrontal_surfavg,R_superiorfrontal_surfavg,R_superiorparietal_surfavg,R_superior temporal_surfavg,R_supramarginal_surfavg,R_frontalpole_surfavg,R_temporalpole_surfavg,R_transverset emporal_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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