Try adding --no-unknown to the label2annot command line
On 02/28/2017 04:45 PM, Antonin Skoch wrote: > 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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
