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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ 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.
