25 Sep
2022
25 Sep
'22
1:06 p.m.
On 9/25/2022 5:06 AM, Mikolaj Pawlak wrote:
External Email - Use Caution
On Fri, Sep 23, 2022 at 4:05 PM Douglas N. Greve dgreve@mgh.harvard.edu wrote:
On 9/22/2022 8:59 AM, Mikolaj Pawlak wrote:External Email - Use Caution Would providing better manual segmentations of those structures of interest help you in building better solutions? I can work with the segmentation that is produced now, but I am interested in improving the results for extracerebral tissues using multimodal imaging and better manual segmentations.
For extra cerebral, you can use the CHARM SAMSEG atlas (https://github.com/simnibs/charm-gems). SAMSEG is already modality agnostic and multimodal, so I'm not sure what you mean there.
The samseg authors used 20 subjects and did not find that increasing that helped all that much (at least on dice scores)That is promising - if the list of those subjects is public and they are part of the oasis dataset as indicated by the paper there is a way to subdivide the segmentation of already existing labels
It may be possible, but won't happen soon.
Can you shed some light on the steps required for creating the current atlas?Unfortunately not. The atlas creation software was the lowest priority of the samseg authors, so it is not easy to run. I myself find it extremely challenging to create new atlases, so I can't support helping others do that. We're trying to get it more streamlined (for you and for us:)I see. If the process can be automated like in multi-atlas label fusion it would be a great way to gain more information about both cerebral and extracerebral tissues. Is building an atlas for T2-weighted images somewhere on the priority list?
again, samseg is already multimodal and modality independent (M3I), so this should not be necessary
thanks, Mikolaj
thanks,Mikolaj On Wed, Sep 21, 2022 at 4:01 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote: by template I'm assuming you mean the atlas. There is not an easy way to create a new atlas or modify the existing one (though we are developing methods to do both). For the eyes, you could probably just write something to look at the column index in the eyes. If it is less than 128, then set it to left otherwise right. On 9/21/2022 6:01 AM, Mikolaj Pawlak wrote:External Email - Use Caution Dear Freesurfers, I have been using samseg for a while and like it a lot. Thank you for this tool. How do you modify the template for this tool? Is there a guideline for this? I would like to divide Fluid_Inside_Eyes label to left and right and improve the bone information in the template. 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