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
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
