Dear experts,
I would like to create modified aparc.a2009s+aseg file with relevant parts of parahippocampal cortical ribbon voxel labels replaced by labels derived from surface labels of entorhinal and parahippocampal cortex (created also by default in recon-all). This modified aparc.a2009s+aseg file I want to use for streamline assignment in structural connectome generation in MrTrix3.
I think that mri_label2vol is not optimal way to do it since it would leave some voxels in the ribbon unassigned.
I think that the better, but much complicated, way to do this is to modify aparc.a2009s.annot with the information from these labels and then run again mris_aparc2aseg.
I tried to do this by using:
mri_annotation2label
and
mris_label2annot --hemi lh --subject my_subject --ldir my_labels --a my_aparc.a2009s --ctab my_aparc.annot.a2009s.ctab --debug
I took the aparc.annot.a2009s.ctab from the my_subject/label directory and added to the end 2 row with entorrhinal and perirhinal parcellations with unique RGB values to assure the relevant parts of parahippocampal gyrus label are replaced by these new labels I want to supply.
But the resulting new .annot file is not correct - the labels are in correct position on cortical surfaces, but the label names of all labels are shuffled.
I even tried the sequence of mri_annotation2label, mris_label2annot without adding new labels, just converting annotation to labels and back, and the annotation naming is also corrupted.
I also tried to create new annotation just from 2 new labels, preparing .ctab file and running mris_label2annot by explicitly specifying my 2 labels like
mris_label2annot --hemi lh --subject my_subject --l lh_labels/lh.perirhinal_exvivo.thresh.label --l lh_labels/lh.entorhinal_exvivo.thresh.label --a rhinal_aparc.a2009s --debug --ctab rhinal_aparc.annot.a2009s.ctab
In this case the label names in annotation are swapped (entorhinal is perirhinal and vice versa), swapped are also file names of labels which I tried to back convert by using mri_annotation2label.
I am using quite recent build of dev version of Freesurfer from 28/2/2017.
Could you suggest where could be the problem?
Or could you advice different, possibly more simple way, how to achieve my goal?
Thank you in advance.
Regards,
Antonin Skoch