Use the --mask option to mri_segstats and pass it a surface overlay with just the cluster of interest in it. You can use --maskthresh and --masksign to fine-tune the masking process.
On 08/15/2018 02:17 PM, Shatil, Anwar Shahadat wrote: > > External Email - Use Caution > > 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 > > > > -------- > > Date: Wed, 15 Aug 2018 11:18:50 -0400 > From: "Douglas N. Greve" <dgr...@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-3cbfbc39b...@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.sha...@sunnybrook.ca > > */This e-mail is intended only for the named recipient(s) and may > contain confidential, personal and/or health information (information > which may be subject to legal restrictions on use, retention and/or > disclosure). No waiver of confidence is intended by virtue of > communication via the internet. Any review or distribution by anyone > other than the person(s) for whom it was originally intended is > strictly prohibited. If you have received this e-mail in error, > please contact the sender and destroy all copies./* > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
