Hello,
Can someone explain how to use the 'split fold control' tool to edit a cortical fold graph sulci. Sometimes sulci do not completely separate and I have tried to use this tool, which works to pixelate the sulci. I can then label each of the halves of the sulci using the labels that are measured for and save the graph. But the problem arises with I do the Morphometric stats. The stats are only provided for the first label used and it gives the measurement for the entire sulci, as if it were not cut at all. Thank you.
Editing sulci using split fold
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riviere
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Re: Editing sulci using split fold
Hi,
The fold split tool in anatomist is not enough alone: it breaks the graph structure and relations. The structure cannot be recomputed on the fly in anatomist, so after the manual folds splits, you have to use the "Cortical folds graph upgrade from old" process in BrainVisa (in the T1MRI toolbox / segmentation pipeline / components, and only visible in "expert" user level). Then, and only then, you can use the morphometry process again.
Denis
The fold split tool in anatomist is not enough alone: it breaks the graph structure and relations. The structure cannot be recomputed on the fly in anatomist, so after the manual folds splits, you have to use the "Cortical folds graph upgrade from old" process in BrainVisa (in the T1MRI toolbox / segmentation pipeline / components, and only visible in "expert" user level). Then, and only then, you can use the morphometry process again.
Denis
Re: Editing sulci using split fold
HI Dennis,
Thank you for responding. I have been using the 3.1 version graph, already upgrading the old graph before I do the split fold tool. So are you saying that I need to do the split fold in the 3.0 graph and then upgrade it after that? That is an easy fix and I can try it out, but I just wanted to clarify before I do anything. Thanks.
Thank you for responding. I have been using the 3.1 version graph, already upgrading the old graph before I do the split fold tool. So are you saying that I need to do the split fold in the 3.0 graph and then upgrade it after that? That is an easy fix and I can try it out, but I just wanted to clarify before I do anything. Thanks.
-
riviere
- Site Admin
- Posts: 1361
- Joined: Tue Jan 06, 2004 12:21 pm
- Location: CEA NeuroSpin, Saint Aubin, France
- Contact:
Re: Editing sulci using split fold
Hi,
Yes, you should re-run the graphs upgrade tool because all relations should be recalculated after a topological change in the graph. Actually in the upgrade process, you should even set the graph_version parameter to 3.2 because the shape of relations after split will change a little bit. If you use the sulcal identification processes afterwards, do not use the older (ANN) ones working on 3.0 graphs because what they have learned does not match this new graphs shape, but you can use the SPAM methods.
Denis
Yes, you should re-run the graphs upgrade tool because all relations should be recalculated after a topological change in the graph. Actually in the upgrade process, you should even set the graph_version parameter to 3.2 because the shape of relations after split will change a little bit. If you use the sulcal identification processes afterwards, do not use the older (ANN) ones working on 3.0 graphs because what they have learned does not match this new graphs shape, but you can use the SPAM methods.
Denis
Re: Editing sulci using split fold
Great! This worked, Thanks!