Region Mapping negative values

[Muhammed Görünen]

Hi TVB users,

I obtained region mapping file from the freesurfer annot files (for Destrieux atlas). There are -1 values in the file. Hence, I cannot load the file to TVB. What can I do for -1 values? (I guess these vertices do not have an associated region in Destrieux atlas) I also have a second question. I have 148 regions. Should region mapping range be 0-147 or 1-148? Thanks in advance.

Best,

--Muhammed

[Lia Domide]

Hi Muhammed,

You could adjust the RM text file in an external tool (e.g. some form of text editor, but also python).

As I see in the FreeSurfer documentation [1] there is an unknown region in the atlas. Its Index could be found by looking into the corresponding Connectivity region names array. Thus, once you find that IDX (for the "unknown") you could replace all -1 values with that IDX.

The range in RM files should be 0 based. Also the IDX of the "unknown" should be computed using the 0 based convention.

[1] https://surfer.nmr.mgh.harvard.edu/fswiki/DestrieuxAtlasChanges

Best,

Lia.

[WOODMAN Michael]

Hi,

The FreeSurferColorLUT.txt file is the reference for meaning of the numbers.  Are there a lot of -1 s?  What  happens when you load the annot file in freeview? Does it have an error there?

cheers,

Marmaduke

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[Muhammed Görünen]

There are 700 -1 among 20484 vertices, but I can succesfully load annot file to freeview. There are 152 regions in total in annot files from rh and lh (including rh'unknown' and lh'unknown'). Four of them do not have a corresponding vertex. I change value of -1s to 0s and enumarate represented 148 regions from 1 to 148. I could load the RM file to TVB with these operations. My weights matrix dimension is 148x148. I wonder if the changes cause a problem in the simulation (maybe regions shift by 1 and vertices correspond to wrong region). 

Best,

--Muhammed

14 Nisan 2022 Perşembe tarihinde saat 10:35:41 UTC+3 itibarıyla marmaduke.woodman şunları yazdı:

[WOODMAN Michael]

hi

If you have -1s from FreeSurfer, you need to sort that out before importing to TVB.  If you verify visually what vertices those are, and you want to ignore them, you can simply create an extra node with zero connectivity and assign the -1 to the index of the new node. 

cheers,

Marmaduke

On 16 Apr 2022, at 21:11, Muhammed Görünen <muhammed...@gmail.com> wrote:

Yes, there are 764 -1s among 20484 vertices. I can succesfully load the file to freeview.