Hi Doug,
using mri_glmfit with DODS and mri_glmfit-sim with a fsgd-file and contrast (attached) that looks like (2 discrete factors: 1 with 2 levels (diagnosis) and 1 with 4 levels (Site) and 1 continuous covariate (age)): GroupDescriptorFile 1 Title AGE-subj Class PatSite1 Class PatSite2 Class PatSite3 Class PatSite4 Class ConSite1 Class ConSite2 Class ConSite3 Class ConSite4 variables Age Input $FSGDID PatSite1 12.8 .. Input $FSGDID PatSite2 9.3 .. Input $FSGDID PatSite3 15.1 .. Input $FSGDID PatSite4 10 .. Input $FSGDID ConSite1 7.6 .. Input $FSGDID ConSite2 8.9 .. Input $FSGDID ConSite3 10.2 .. Input $FSGDID ConSite4 14 ..
mri_glmfit --y lh.justmen.NOTmatched.CT.fwhm10.mgh --fsgd fsgd_justmen_NOTmatched_only_age.txt --C contrast_justmen_DODS_GxA.mtx --surf fsaverage lh --cortex --glmdir lh.justmen.NOTmatched.all.GRxAge.CT.fwhm10
for the contrast attached (which i thought is the interaction between diagnosis and age, independent of 'Site') i found 3 clusters using mri_glmfit-sim (attached). i saved these clusters as labels and transformed them to native space (cluster appeared in the correct location in native space): mri_label2label --srclabel cluster-001.label --srcsubject fsaverage --trgsubject $subject --trglabel $subject_cluster-001.label --regmethod surface --hemi lh
and extracted mean CT from the cluster in native space: mris_anatomical_stats -l $subject_cluster-001.label -t lh.thickness -b -f $subject_cluster-001.stats $subject
i plotted mean thickness for each cluster against age but did *not* see an interaction between groups. even though this is mean thickness for the cluster on non-smoothed native space thickness i would have expected to see some interaction but the slopes for both groups are almost parallel. any thoughts? i can provide more info if needed. -joost
Hi Joost, I'm a little lost. Are you doing the initial mri_glmfit analysis on thickness or CT? doug
On 03/05/2013 03:31 AM, j janssen wrote:
Hi Doug,
using mri_glmfit with DODS and mri_glmfit-sim with a fsgd-file and contrast (attached) that looks like (2 discrete factors: 1 with 2 levels (diagnosis) and 1 with 4 levels (Site) and 1 continuous covariate (age)): GroupDescriptorFile 1 Title AGE-subj Class PatSite1 Class PatSite2 Class PatSite3 Class PatSite4 Class ConSite1 Class ConSite2 Class ConSite3 Class ConSite4 variables Age Input $FSGDID PatSite1 12.8 .. Input $FSGDID PatSite2 9.3 .. Input $FSGDID PatSite3 15.1 .. Input $FSGDID PatSite4 10 .. Input $FSGDID ConSite1 7.6 .. Input $FSGDID ConSite2 8.9 .. Input $FSGDID ConSite3 10.2 .. Input $FSGDID ConSite4 14 ..
mri_glmfit --y lh.justmen.NOTmatched.CT.fwhm10.mgh --fsgd fsgd_justmen_NOTmatched_only_age.txt --C contrast_justmen_DODS_GxA.mtx --surf fsaverage lh --cortex --glmdir lh.justmen.NOTmatched.all.GRxAge.CT.fwhm10
for the contrast attached (which i thought is the interaction between diagnosis and age, independent of 'Site') i found 3 clusters using mri_glmfit-sim (attached). i saved these clusters as labels and transformed them to native space (cluster appeared in the correct location in native space): mri_label2label --srclabel cluster-001.label --srcsubject fsaverage --trgsubject $subject --trglabel $subject_cluster-001.label --regmethod surface --hemi lh
and extracted mean CT from the cluster in native space: mris_anatomical_stats -l $subject_cluster-001.label -t lh.thickness -b -f $subject_cluster-001.stats $subject
i plotted mean thickness for each cluster against age but did *not* see an interaction between groups. even though this is mean thickness for the cluster on non-smoothed native space thickness i would have expected to see some interaction but the slopes for both groups are almost parallel. any thoughts? i can provide more info if needed. -joost
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Douglas N Greve -
j janssen