Hi, To run bbregister outside of the recon stream, I tried: setenv SUBJECTS_DIR /autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR cd $SUBJECTS_DIR bbregister --mov mri/nu.mgz --int ../mni305.cor.mgz --reg mri/transforms/talairachTEST.xfm --init-spm --t1 --s amac_TEST --tmp ./TEMP
but when I tried to view it with: tkregister2 --mov amac_TEST/mri/nu.mgz --fstal --reg amac_TEST/mri/transforms/talairachTEST.xfm --surf orig --s amac_TEST It looks the same as it did before, and I am concerned that the bad tal registration will affect the localization of fMRI data and ICV measurements. Does anyone have any advice on how to fix the registration? Thanks, Garth > > -- > > On Tue, 16 Mar 2010, Garth Coombs wrote: > >> Hi, >> >> I recently ran into a problem with some of my tal registrations during the >> recon-all process (see below message to Martino's Tech). In order to fix the >> problem, it was suggested that we run bbregister outside of the recon-all >> stream and then feed that registration into the subsequent recon stages. >> Does this make sense, and how would I go about doing this? I'm not sure what >> the --mov file should be, or if there is a way to specify fstal as the >> reference structural. >> >> Thanks for your help! >> >> -Garth >> >> Hi Doug & FreeSurfers, >> >> I recently re-ran a large number of recons and have been checking to make >> sure >> they all ran correctly, and I have come up with a couple of questions about >> the >> talairach transform/recon checking. >> >> For some of my recons, the green line outlining the white matter on the >> individual brain extends slightly further than the cortex surface of the >> fstal >> brain. While it looks relatively well aligned (e.g. ventricles, brain stem), >> the >> fstal brain looks slightly too small for the subject's brain. Additionally, >> the >> green outline tends to extend into the skull of fstal in the sagittal plane. >> An >> example is: >> >> setenv SUBJECTS_DIR /autofs/space/brownie_003/users/gcoombs/SUBJECTS_DIR/ >> tkregister2 --mgz --fstal --surf orig --s amac_anat >> >> or >> >> tkregister2 --mgz --fstal --surf orig --s amra_anat >> >> In order to fix these talairach transforms, it seems like the best option >> would >> be to scale the brain; however, we will be doing a cortical thickness >> analysis >> on this group, and we do not want to scale the brain if it will somehow >> affect >> the outcomes. Is this something we should worry about? >> >> Another question we have is about general recon quality control: when >> checking >> that the recons ran smoothly, what should we look for? I look to make sure >> that >> the pial and white matter surface lines don't include dura or any other >> matter >> and that they follow the structures correctly, skull stripping, and intensity >> normalization, but is there anything else that is particularly important? >> >> Any advice would be greatly appreciated! >> >> Thanks, >> Garth >> > >
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