Hi Guang, even in the longitudinal stream the asegs (and all images) are in the TP native space. They still need to be registered (either to each other or to the base space). The base space is recommended, because that way both images are treated the same (both are resampled). The registrations are available in the base directory baseid/mri/transforms.
Here is the corresponding passage from the WIKI page http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing --------------------------- It is possible to check the registrations and template creation either using the norm.mgz or orig.mgz of all time points. These images are first mapped to and resampled in the space of the base with: mri_convert -rl <baseid>/mri/norm.mgz -at <baseid>/mri/transforms/<tpNid>_to_<baseid>.lta <tpNid>/mri/norm.mgz <tpNid>_to_<baseid>.norm.mgz The resampled files <tpNid>_to_<baseid>.norm.mgz can than be compared with each other or with the base's norm_template.mgz using e.g. tkmedit -f file1 -aux file2. If you want to compare aseg.mgz files, make sure, you use nearest for the resample type: mri_convert -rl <baseid>/mri/aseg.mgz -rt nearest -at <baseid>/mri/transforms/<tpNid>_to_<baseid>.lta <tpNid>/mri/aseg.mgz <tpNid>_to_<baseid>.aseg.mgz ---------------------------- good luck, Martin On Wed, 2009-09-23 at 13:54 -0500, Guang Zeng wrote: > I think I still need register the second tp aseg.mgz to the first tp > aseg.mgz, even they are longitudinal-stream analyzed. > The dice coefficients are higher after registration. > > > ______________________________________________________________________ > From: freesurfer...@hotmail.com > To: ni...@nmr.mgh.harvard.edu > Date: Wed, 23 Sep 2009 13:04:59 -0500 > CC: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] how to use mri_compute_seg_overlap > > Hello, Nick, > > Yes, I can get the results now, I set the wrong path. > > Just want to double check, > I have send the two subjects (from different time points) to the > FreeSurfer longitudinal stream, > so the resulted two aseg.mgz files have been registered to the > base-template, right? > > Thanks a lot! > Guang > > > > From: ni...@nmr.mgh.harvard.edu > > To: freesurfer...@hotmail.com > > Date: Wed, 23 Sep 2009 13:01:52 -0400 > > CC: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] how to use mri_compute_seg_overlap > > > > Guang, > > > > So you did not get output that looked like this? > > > > logging overall Dice to text > > Jaccard Coefficients: > > correct ratio for label 2 = 1 > > correct ratio for label 41 = 1 > > . > > . > > correct ratio for label 44 = 1 > > mean +/- std = 1.0000 +/- 0.0000 > > Dice Coefficients: > > label 2 = 1 > > label 41 = 1 > > . > > . > > . > > label 44 = 1 > > mean +/- std = 1.0000 +/- 0.0000 > > Overall subcortical dice = 1.0000 > > > > (in this example, i compared the same aseg, so dice will be 1). > > > > also, make sure your second time point aseg is registered to the > first. > > if it is not, the your dices will be low, because its just comparing > > voxel to voxel. > > > > Nick > > > > > > On Wed, 2009-09-23 at 11:30 -0500, Guang Zeng wrote: > > > Hi, there, > > > > > > I have two subjects from two time points, I'd like to compare > their > > > overlap ratio of FreeSurfer segmented hippocampus. > > > I try to use the command mri_compute_seg_overlap to do it, > > > > > > My command line is: > > > mri_compute_seg_overlap -olog text tp1/mri/aseg.mgz > tp2/mri/aseg.mgz > > > > > > Is it correct? I ran it, but nothing happen. > > > > > > Thanks! > > > > > > Guang > > > > > > > > > > > > > ______________________________________________________________________ > > > Insert movie times and more without leaving Hotmail®. See how. > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ______________________________________________________________________ > Insert movie times and more without leaving Hotmail®. See how. > > ______________________________________________________________________ > Insert movie times and more without leaving Hotmail®. See how. > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
