I think that is a good method (better than the method I just sent).
On 03/03/2017 07:12 PM, Antonin Skoch wrote: > Dear experts, > > concerning my question regarding thresholding method of entorhinal and > perirhinal labels, I looked at > > Augustinack JC et al, Predicting the location of human perirhinal > cortex, Brodmann's area 35, from MRI, Neuroimage 2013 Jan 1;64:32-42. > > where I found the text: > > For each label, the vertices were ordered from most probable least > probable), then thresholded so that the surface area of each predicted > entorhinal cortex or perirhinal cortex label matched the average > surface area of the ex vivo labels. > > So, if I understand it correctly, at least for the entorhinal and > perirhinal *thresh labels, the threshold has been found individually > for each label and hemisphere separately, so that the area of the > label in the fsaverage space match average surface area of the > corresponding ex-vivo labels? > Therefore, no restriction for overlap of perirhinal and entorhinal > labels was applied in the thresholding? I found that in the right > hemisphere the rh.entorhinal_thresh.label almost completely overlaps > with lh.entorhinal_thresh.label. > > But, for generating custom aparc+aseg I need non-overlapping labels. I > attempted to resolve the issue by using > > mris_label2annot --s fsaverage --l > fsaverage/label/lh.entorhinal_exvivo.label --l > fsaverage/label/lh.perirhinal_exvivo.label --hemi lh --ctab > entorhinal_perirhinal.annot.ctab --maxstatwinner --thresh 0.4 --a > entorhinal_perirhinal_thresh_0.4 > > i.e. using --maxstatswinner and --thresh 0.4 which gives > non-overlapping labels with shapes approximately similar to the > original entorhinal_exvivo.thresh.label and > perirhinal_exvivo.thresh.label, but it probably violates the condition > of similar area extent. > > Could you please comment on if my used method is acceptable, or > suggest better method how to achieve non-overlaping entorhinal and > perirhinal labels for the purpose of generating custom aparc+aseg from > them? > > Regards, > > Antonin Skoch > > Dear experts, > > Could you please provide me the information how exactly the > *_exvivo.thresh.labels have been thresholded? > According to this post, > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg32542.html > .thresh labels are thresholded to pick the most likely vertices that give a > label that is > the right surface area.But how they are thresholded in the boundary of the > region where the unthresholded labels do not overlap? There must be additional > threshold applied: > For example for BA45 there is no further BA label towards frontal pole, but > the > BA45_exvivo.thresh.label is also restricted in this region wrt > BA45_exvivo.label. > > I have further question concerning used thresholding method of > perirhinal_exvivo.thresh and entorhinal_exvivo.thresh labels. It seems that > this method is not applied here since looking at them at the fsaverage > surface, > they are overlapping. And also *rhinal_exvivo.labels are much more extending > to > the adjacent regions than *rhinal_exvivo.thresh.labels. What method is applied > here? > > My main objective to obtain annotation with the vertices properly assigned to > perirhinal_exvivo and entorhinal_exvivo to supply this annotation to > mri_aparc2aseg to assign ribbon voxels to that parcellation. I think I could > use mris_label2annot --maxstatswinner with unthresholded entorhinal and > perirhinal labels to assign vertices to most probable label, but I would need > to further threshold the labels by correct value to obtain results similar in > extent to thresh.labels. > > For perirhinal, it seems that the additional threshold is 0.4 (what is > rationale for this value?), for entorhinal it seems also around 0.4 but could > not find any particular threshold to obtain the exact shape of label > corresponding to entorhinal_exvivo.thresh. > > Thank you in advance for clarification. > > Regards, > > Antonin Skoch > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. 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