Hi Venkat,

are you using version 5.1 ? In earlier versions, time points were not aligned to the base, so they don't align. Since 5.1 they should perfectly align. If not it can have several reasons. The most common reason is that skull strip fails in the cross sectional runs. Large chunks of skull can throw off the registration in the base.

In your case, you have only 2 time points and an error in the registration would immediately result in a messed up norm.mgz image in the base:

nonhyper_24_templ/mri/norm.mgz would be very blurry or show two ghost images.

So take a look at that and also the skull strip in nonhyper_24_06/mri/brainmask.mgz nonhyper_24_07/mri/brainmask.mgz

and fix them if it they are bad.

Best, Martin

On Thu, 2012-08-02 at 13:48 -0400, Rajagopalan, Venkateswaran wrote:

Dear All,

I ran the following steps in a patient of mine at two time points nonhyper_24_06 and nonhyper_24_07

recon-all -autorecon1 -subjid nonhyper_24_06 recon-all -autorecon1 -subjid nonhyper_24_07 recon-all -autorecon2 -subjid nonhyper_24_06 recon-all -autorecon3 -subjid nonhyper_24_06 recon-all -autorecon2 -subjid nonhyper_24_07 recon-all -autorecon3 -subjid nonhyper_24_07

# template creation

recon-all -base nonhyper_24_templ -tp nonhyper_24_06 -tp nonhyper_24_07 -all

recon-all -long nonhyper_24_06 nonhyper_24_templ -all recon-all -long nonhyper_24_07 nonhyper_24_templ -all

When I tried to inspect my longitudinal result using freeview -v nonhyper_24_06.long.nonhyper_24_templ/mri/norm.mgz \ nonhyper_24_07.long.nonhyper_24_templ/mri/norm.mgz \ -f nonhyper_24_06.long.nonhyper_24_templ/surf/lh.pial:edgecolor=red \

nonhyper_24_06.long.nonhyper_24_templ/surf/lh.white:edgecolor=blue \

nonhyper_24_07.long.nonhyper_24_templ/surf/lh.pial:edgecolor=255,128,128 \

nonhyper_24_07.long.nonhyper_24_templ/surf/lh.white:edgecolor=lightblue

My norm images from two time points doesn't overlap (so does the pial and white surfaces from two points they appear on two distinct places on the freeview instead of being overlaped as shown in tutorial) when I load then it looks like there is some registration problem. I don't know where I made a mistake and how to correct for this. Any help will be greatly appreciated.

Thanks Venkat

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