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Question re. importing individual anatomy

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Posts: 3
Topic starter
(@guyrens)
New Member
Joined: 3 years ago

Hi all,

 

I am trying to import a segmented head file which I generated using FreeSurfer.

The steps I undertake are starting from the AtlasViewerGUI:

File > Import MRI anatomy (opens additional GUI) > click browse on the segmented head line > open the [hseg.mgz] file from my participant.

 

Importing the file seems to work fine, but I run into the following issue:

---

Note: No ref points file found in C:/Users/guy_r/Documents/GitHub/AtlasViewer/anatomical/
Index exceeds matrix dimensions.

Error in preRegister (line 25)
ap = refpts.pos(1,:);

Error in getProbe (line 110)
probe = preRegister(probe, headsurf, refpts);

Error in AtlasViewerGUI>LoadSubj (line 178)
probe = getProbe(probe, dirnameSubj, digpts, headsurf, refpts, currElem);

... (some other error lines which may be less relevant)

----

If I am right, AtlasViewer is trying to call to a digpts file which does not exist.

Currently I do not have a montage for this participant as I was just trying to load in the anatomy and then make a custom montage in AtlasViewer.

 

So my question is: is there a way of loading the segmented file (from FreeSurfer) directly into AtlasViewer without dgpts.txt file. 

If not, how can I make an arbitrary dgpts.txt file that enables me to load in the segmented file?

 

Many thanks in advance

 

Guy

4 Replies
Posts: 309
(@dboas)
Joined: 4 years ago

Thanks for pointing out this workflow issue. It would be nice if that just worked the way you wanted. But for now you can take the following steps that should work:

make your montage on the default colin atlas in a new and empty folder. Then save that SD file in a new folder that is empty. Then you can run atlasviewer in that directory and import the segmented MRI file. The SD file should register to the new MRI using the anchor points you defined in the montage.

Note, I see that you ran atlasviewer in the atlasviewer root directory in your example. You should really never do that. Always create a separate new directory to do your work in.

Also note, we are beta testing a new way of making montages on the 3D head directly. It seems to be working very well and will help you with this process. That will be released soon.

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1 Reply
(@guyrens)
Joined: 3 years ago

New Member
Posts: 3

@dboas

Normally I generate my montages in NirX using their software. I am able to export their montage as a digpts.txt file and use that load in the correct in atlasviewer.

Is there a way for me to do what you described but use the digpts.txt file instead of the .sd file? As of now, this does not seem to work?

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Posts: 3
Topic starter
(@guyrens)
New Member
Joined: 3 years ago

I just noticed the first paragraph is not really understandable. To clarify:

 

Normally I generate my montages in NirX using their software. When the montage is designed, I can export it as a digpts.txt file. This digpts.txt file can be loaded into AtlasViewer to generate the montage over the head of a template brain.

Is there a way for me to do what you described but use the digpts.txt file instead of the .sd file? As of now, this does not seem to work..

So: can I load the hseg.mgz combined with the digpts.txt file in order to load individual anatomies into AtlasViewer?

 

Many thanks

 

Guy

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Posts: 309
(@dboas)
Joined: 4 years ago

In the first post you said you did not have a digpts.txt file. It sounds like you are able to do what you say you want to do in your last post, which is not what you said in the first post is the problem that you are having

 

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