External Email - Use Caution
Hi experts,
Will you please confirm below command lines I run to examine between group differences in LGI? I have 3 questions listed.
I can’t run the below line, it gives an error:
mris_preproc --fsgd TDvsNDDageSAsex.fsgd --cache-in lh.pial_lgi.fwhm0.fsaverage --target fsaverage --hemi lh --meas pial_lgi --out lh.pial_lgi.0.mgh
mris_preproc --fsgd TDvsNDDageSAsex.fsgd --cache-in rh.pial_lgi.fwhm0.fsaverage --target fsaverage --hemi rh --meas pial_lgi --out rh.pial_lgi.0.mgh
Therefore, I run the below line instead - although I know it’s for uncached data and I have already ran qcache for my subjects (using: recon-all -s 101031_01 -qcache -measure pial_lgi)
mris_preproc --fsgd ASDvsADHD.txt --target fsaverage --hemi lh --meas pial_lgi --out lh.pial_lgi.mgh
mri_surf2surf --hemi lh --s fsaverage --sval lh.pial_lgi.mgh --fwhm 0 --cortex --tval lh.pial_lgi.0.mgh
# I run above line separately for right hemisphere
1. Do I have to write “cortex” in above command line or not?
2. Is it okay to run this command line considering that qcache has already been run on all my subjects?
3. I’ve ran qcache (and above command line) multiple times on each subject in my data. Is this ok? Or does this mess up anything?
To test for main effect of group, I ran below line:
mri_glmfit --y lh.pial_lgi.0.mgh --fsgd ASDvsADHD.txt dods --C betweengroupdifferencecontrollingforageSAsex.mtx --C agebydiagnosisinteraction.mtx --surf fsaverage lh --cortex --glmdir lh.ASDvsADHD.glmdir
mri_glmfit --y rh.pial_lgi.0.mgh --fsgd ASDvsADHD.txt dods --C betweengroupdifferencecontrollingforageSAsex.mtx --C agebydiagnosisinteraction.mtx --surf fsaverage rh --cortex --glmdir rh.ASDvsADHD.glmdir
To correct for multiple comparisons using monte carlo:
mri_glmfit-sim --glmdir lh.ASDvsADHD.glmdir --cache 1.3 abs --cwp 0.05 --2spaces
mri_glmfit-sim --glmdir rh.ASDvsADHD.glmdir --cache 1.3 abs --cwp 0.05 --2spaces
I'd really appreciate your soon reply,
Thanks so much for all your support,
Avi