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Hi Doug:


Thanks for your reply. I think you are correct.


Is there any way to extract the number of vertices from the cluster spanning each of Yeo's 7 networks? I tried to overlay Yeo2011_7Networks_N1000.annot on the .mgh file and use my cursor to get information, but that does not give me the number of vertices.


Thanks,

Anwar



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Date: Wed, 15 Aug 2018 11:18:50 -0400
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Extracting number of vertices in Yeo's
        7Networks from significant clusters
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <0870c8a6-0a29-b748-500a-3cbfbc39b8f0@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"; format=flowed

The input (--i) only supplies information for use in computing the Mean, 
StdDev, etc. The number of vertices willcome from the annot. Or am I 
misunderstanding something?
From: Shatil, Anwar Shahadat
Sent: August 15, 2018 10:44 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Extracting number of vertices in Yeo's 7Networks from significant clusters
 

Hello Doug and other experts:


I have done QDEC analysis between two groups (healthy controls vs disease) and obtained different .mgh and .annot files. I got one big cluster covering most part of the brain. I wanted to extract the number of vertices for Yeo's 7 Networks in that big cluster and therefore I ran this:


mri_segstats --i cache.th30.pos.sig.masked.mgh --annot fsaverage rh Yeo2011_7Networks_N1000 --excludeid 0 --sum network_param.dat

The result was:

Col Headers  Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range  
  1   1     22519    14950.0  7Networks_1                        1.4816     1.8126     0.0000     3.6990     3.6990 
  2   2     30207    12514.7  7Networks_2                        2.6658     1.6596     0.0000     3.6990     3.6990 
  3   3     17604     8224.3  7Networks_3                        2.6278     1.6778     0.0000     3.6990     3.6990 
  4   4     19402     8357.2  7Networks_4                        3.3453     1.0877     0.0000     3.6990     3.6990 
  5   5     11614     6205.0  7Networks_5                        2.1434     1.7750     0.0000     3.6990     3.6990 
  6   6     22330    12170.7  7Networks_6                        2.6315     1.6761     0.0000     3.6990     3.6990 
  7   7     26056    13826.2  7Networks_7                        3.0249     1.4229     0.0000     3.6990     3.6990 

I ran the same code for different --i (input) .mgh files and everytime the NVertices were the same, which means this is not the one I am looking for. 

Can you please help me in getting the number of vertices of Yeo's each network that fall in that big cluster?

Thanks.

Anwar


--

Anwar S. Shatil

Research Assistant
Department of Medical Imaging
Sunnybrook Health Sciences Centre
Room AB204, 2075 Bayview Avenue
Toronto, ON M4N 3M5
Tel: 416.480.6100 ext. 89617
Email: anwar.shatil@sunnybrook.ca

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