Hi Antonin, where did you upload them to?

On 03/13/2017 05:51 PM, Antonin Skoch wrote:
> Dear experts,
>
> in my longitudinal study with 2 timepoints I encountered issue with 
> aseg.presurf labeling and white/pial surface estimation of one subject 
> in region of occipital horns of lateral ventricle. The voxels in horns 
> are mislabeled as either white or gray matter or contain zero values.
> I am still in the stage 1 of longitudinal stream, so this is classical 
> cross-sectional recon-all stream.
>
> I tried to reprocess this subject by using recon-all -s subj 
> -bigventricles -FLAIRpial (despite the fact that the subject does not 
> have generally enlarged ventricles I thought that this could help 
> nonlinear registration by mri_ca_register ). In case of timepoint 2 
> this helped to correctly label left occipital horn and corrected error 
> with surfaces, but right occipital horn remained labeled as white matter.
>
> In contrast, in case of timepoint 1 the -bigventricles did not help to 
> label left occipital horn and additionally new massive error with 
> white surface placement appeared in the region of occipital horn of 
> left lateral ventricle. See the attached screenshots to ilustrate this 
> issue:
>
> tp1_nobigventricles_surface_OK
> tp1_bigventricles_surface_error
> tp2_nobigventricles_surface_error
> tp2_bigventricles_surface_OK
>
> I have uploaded file 
> occipital_horn_ventricle_aseg_and_surf_error.tar.gz containing 4 
> recons (timepoint 1 and 2 with and withoug -bigventricles) to your server.
>
> I suppose that the root of the problem is incorrect nonlinear 
> registration. Could you please advise how to diagnose and solve the error?
>
> I am using development version from beginning of february 2017.
>
> Regards,
>
> Antonin Skoch
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