When you say that you are getting very different results, what are you
comparing exactly? I can't tell what your mri_glmfit command is because
it is embedded in a script with lots of variables. Have mercy on me and
just give me a simple command line that I don't have to struggle with:)
doug
On 11/05/2013 02:21 PM, Jonathan DuBois wrote:
> Hi All,
>
> In a previous post Doug suggested two methods for generating
> voxel-wise z-score maps, one using glmfit with one subject in one
> group and the second using fscalc.fsl. Link to post:
> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-June/014673.html
>
>
> I have tried both methods using PET data registered to the surface,
> but get very different results from fscalc and mri_glmfit. The results
> I expect are given by fscalc, but I would also like to run the Monte
> Carlo-based MCC, which requires a glmdir. Is there another way to run
> MC MCC on the z-map generated by fscal or alternatively, is the code
> that I am using for glmfit wrong? A simplified version of the code for
> both analyses is below. I am using FS 5.3 with the fsl binaries from
> the release notes on mac OS 10.8.
>
>
> Thanks for your help
> Jon
>
> --mri_glmfit:
> for h in rh lh; do mris_preproc --target fsaverage --hemi $h --iv
> nc01_mrispace_pet.mgz nc01_mrispace_pet_2_T1_register.dat --iv
> nc02_mrispace_pet.mgz nc02_mrispace_pet_2_T1_register.dat --iv
> nc03_mrispace_pet.mgz nc03_mrispace_pet_2_T1_register.dat --iv
> pat01_mrispace_pet.mgz pat01_mrispace_pet_2_T1_register.dat --pf 0.5
> --out ${h}.pat01_allcontrols_pet_ztest_pf05_fsaverage.mgh
>
> for h in rh lh; do mri_surf2surf --hemi $h --s fsaverage --fwhm 10
> --cortex --sval
> ${h}.${s}pat01_allcontrols_pet_ztest_pf05_fsaverage.mgh --tval
> ${h}.${s}pat01_allcontrols_pet_ztest_pf05_fsaverage_fwhm10.mgh; done
>
> for h in rh lh; do mri_glmfit --y
> ${h}.${s}pat01_allcontrols_pet_ztest_pf05_fsaverage_fwhm10.mgh --fsgd
> patient1_allcontrols_ztest.fsgd dods --C group2_cov0_diff.mtx --surf
> fsaverage $h --cortex --glmdir
> ${h}.${s}pat01_allcontrols_pet_ztest_pf05_fsaverage_fwhm10.glmdir
>
> *patient1_allcontrols_ztest.fsgd*:
> GroupDescriptorFile 1
> Title patient01_ztest
> Class Patient
> Class Control
> Input pat01 Patient
> Input nc01 Control
> Input nc02 Control
> Input nc03 Control
>
> *group2_cov0_diff.mtx*:
> -1 1
>
> --fscalc.fsl:
> for h in rh lh; do mris_preproc --target fsaverage --hemi $h --iv
> nc01_mrispace_pet.mgz nc01_mrispace_pet_2_T1_register.dat --iv
> nc02_mrispace_pet.mgz nc02_mrispace_pet_2_T1_register.dat --iv
> nc03_mrispace_pet.mgz nc03_mrispace_pet_2_T1_register.dat --pf 0.5
> --out ${h}.allcontrols_pet_ztest_pf05_fsaverage.mgh
>
> for h in rh lh; do mris_preproc --target fsaverage --hemi $h --iv
> pat01_mrispace_pet.mgz pat01_mrispace_pet_2_T1_register.dat --pf 0.5
> --out ${h}.patient01_pet_ztest_pf05_fsaverage.mgh
>
> for h in rh lh; do for stat in mean std; do mri_concat
> ${h}.allcontrols_pet_ztest_pf05_fsaverage.mgh --o
> ${h}.allcontrols_pet_ztest_pf05_fsaverage_${stat}.mgh --${stat}; done;
> done
>
> for h in rh lh; do fscalc.fsl --surf fsaverage $h
> ${h}.patient01_pet_ztest_pf05_fsaverage.mgh -sub
> ${h}.allcontrols_pet_ztest_pf05_fsaverage_mean.mgh -div
> ${h}.allcontrols_pet_ztest_pf05_fsaverage_std.mgh
> ${h}.patient01_vs_allcontrols_pet_ztest_pf05_fsaverage_zmap.mgh; done
>
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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