Are those maps corrected for multiple comparisons or uncorrected? If corrected, how similar are the uncorrected? When doing a correction, you can get clusters that are just above significance in one analysis and just below sig in the other making it look like there are huge differences. I've looked at a bunch of FDG data comparing spmregister and bbregister and not found a big difference. Having said that, I think that spmregister in general does a better job on smooth images. I wrote my own version (not reliant on matlab or spm) called mri_coreg, which you can get from here
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg On 03/31/2016 02:44 PM, Alshikho, Mohamad J. wrote: > > Hi Doug, > > In order to run surface based analysis on PET maps, _I used the > following steps: _ > > *_1. Co-registering SUVR to T1_* > > bbregister --s name --mov suvr.nii --bold --init-fsl --reg reg.dat --o > suvr_T1.mgh > > *_2. Concatenate SUVR maps_* > > mris_preproc --target fsaverage --hemi lh --iv > subject1/suvr/suvr_T1.mgh subject1/suvr/reg.dat --iv > subject2/suvr/suvr_T1.mgh subject2/suvr/reg.dat --iv … --projfrac 0.5 > --out lh.suvr.mgh > > *_3. Smoothing(sm)_* > > mri_surf2surf --hemi lh --s fsaverage --fwhm 10 --cortex --sval > lh.suvr.mgh --tval lh.suvr.sm10.mgh > > *_4.Group analysis (GLM)_* > > mri_glmfit--y lh.suvr.sm10.mgh --fsgd fsgd.txt --C X.mtx --surf > fsaverage lh --cortex --glmdir lh.suvr > > *_5. Correction for multiple comparisons ( Cluster –wise)_* > > mri_glmfit-sim --glmdir lh.suvr --cache 1.3 neg --cwp 0.05 --2spaces > # Cache 1.3 ( P<0.05) > > ·In a second analysis for the same set of data, I replaced the first > step ( co registration) by the following command line: > > spmregister --s name --mov suvr.nii --reg reg.dat --o suvr_T1.mgh > > I got the results as attached ( figure1 using bbregister and figure 2 > using SPM register) > > Kindly, > > 1.Where this difference came from? In other words, should I expect > such like difference between “bbregister” and “spmregister” ? > > 2.For co registration which command do you recommend “bbregister” or > “spmregister” ? > > Best, > > Mohamad > > > > _______________________________________________ > 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.
