Dear experts,

I am testing the longitudinal stream with V6beta version.

The recon-all -help says for -noasegfusion:

Do not create 'fused' aseg from the longbase timepoints, which would normally
be used to initialize the ca_labeling.  Instead, initialize using the longbase
aseg.mgz.

As I looked to recon-all code it seems that in case of -noasegfusion there is no use of -r and -ri parameters and therefore no "initialization".  Could you please comment on?

My second query is regarding manual edits:

In one subject the manual editing of aseg was necessary due to ventricle mislabeling. I edited the aseg.presurf in base template and subsequently run longitudinal stream via

recon-all -long tpID templateID -noasegfusion -all

From the last sentence of -noasegfusion help I (wrongly) expected that my aseg.presurf edits in base template would be incorporated for -long recon. However, this was not the case, the edits have not been incorporated at all. Looking at the recon-all code the aseg.presurf from base is never used for -long.

I thought that I could incorporate manual edits from base by manual copying of aseg.presurf from base to long directory. As I looked for the way how the manual aseg edits are handled in recon-all, they are identified by using the difference between the files aseg.auto and aseg.manedit which contains manual edits. Therefore I think that the copying from base is not an option, I expect that this would replace segmentations not only in manual edit regions, but in all regions where the aseg.auto of base and aseg.auto of -long differs (they do not have the same input) which is undesirable. So I think I do not have any other option than to edit aseg.presurf in -long again.

Could you please comment on how to optimally handle such situations?

Regards,

Antonin Skoch