Creating custom aparc.a2009s+aseg.mgz: Shuffled names of parcellations after mris_label2annot
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
Hi Antonin, I've verified the problem and am working on a solution.
doug
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
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
freesurfer@nmr.mgh.harvard.edu
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Antonin Skoch -
Douglas N Greve