Hi Douglas,
Sorry about that! I hope this works. I have pasted the earlier correspondence here with your response below: Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+Extracting+MNI+Coordinates+from+the+Destrieux+Atlas%5C%3A+Checking+steps%22&o=newest> Douglas N Greve <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22> Wed, 12 Aug 2015 07:27:49 -0700 <http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20150812> Those are more-or-less talairach coords, not MNI. If you add --nofixmni, the results will be reported in mni305 coords. Those are more-or-less talairach coords, not MNI. If you add --nofixmni, the results will be reported in mni305 coords. On 08/10/2015 08:39 AM, Elijah Mak wrote: > Hi Freesurfer Experts, > > For the purpose of defining nodes in a graph theory analysis, I would > like to generate a list of X Y Z coordinates in MNI space for all the > labels in the Destrieux atlas. I came across a previous post with the > following steps: > > Step 1: > > mri_annotation2label --subject fsaverage --hemi lh --annotation > aparc.a2009s --outdir /Users/ElijahMak > > Step 2: > > mri_surfcluster --in > /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel > lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin > --centroid --thmin 0 --hemi lh --subject fsaverage > > > Everything went smoothly, but I would like to check my steps with you before > I proceed to generate the coordinates individually for each ROI per > hemisphere. > > > The output from #2 issum.lh.G_and_S_frontomargin. When I load it, I see > > dhcp-172-17-218-173:~ ElijahMak$ cat sum.lh.G_and_S_frontomargin > > > # Cluster Growing Summary (mri_surfcluster) > > > # $Id: mri_surfcluster.c,v 1.51.2.3 2012/05/31 22:10:05 greve Exp $ > > > # $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ > > > # CreationTime 2015/08/10-12:29:31-GMT > > > # cmdline mri_surfcluster --in > /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness --clabel > lh.G_and_S_frontomargin.label --sum sum.lh.G_and_S_frontomargin > --centroid --thmin 0 --hemi lh --subject fsaverage > > > # cwd /Users/ElijahMak > > > # sysname Darwin > > > # hostname dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk > <http://dhcp-172-17-218-173.eduroam.wireless.private.cam.ac.uk> > > > # machine x86_64 > > > # FixVertexAreaFlag 1 > > > # FixSurfClusterArea 1 > > > # > > > # Input /Applications/freesurfer/subjects/fsaverage/surf/lh.thickness > > > # Frame Number 0 > > > # srcsubj fsaverage > > > # hemi lh > > > # surface white > > > # SUBJECTS_DIR /Applications/freesurfer/subjects > > > # SearchSpace_mm2 65416.6 > > > # SearchSpace_vtx 932 > > > # Bonferroni 0 > > > # Minimum Threshold 0 > > > # Maximum Threshold infinity > > > # Threshold Sign abs > > > # AdjustThreshWhenOneTail 1 > > > # Area Threshold 0 mm^2 > > > # clabelfile lh.G_and_S_frontomargin.label > > > # clabelinv 0 > > > # Overall max 3.33248 at vertex 83949 > > > # Overall min 0 at vertex 0 > > > # NClusters 1 > > > # Total Cortical Surface Area 65416.6 (mm^2) > > > # FixMNI = 1 > > > # > > > # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ NVtxs > > 1 3.332 83949 82219.39 -29.4 -22.0 17.4 163842 > > > > > Are those TalX TalY TalZ the values I'm looking for? > > > Many thanks for your time. > > > Best Wishes, > Elijah > > > -- > > Elijah Mak, > > PhD Candidate *|* Psychiatry > > University of Cambridge > > Trinity College, Cambridge, CB2 1TQ > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR centergr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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 athttp://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. On Mon, Aug 17, 2015 at 4:23 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu> wrote: sorry, what is this in reference too? Please remember to include the text from previous exchanges so we have context for questions. We answer a lot of email on freesurfer@... and it is hard to keep track of things. On 8/14/15 7:00 AM, Elijah Mak wrote: Hi Douglas, Thanks for the help! However, when I tried the --nofixmni flag, all the ROIs appeared to have identical MNI coordinates. I have pasted the output from 3 ROIS in the LH. # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ NVtxs 1 3.332 83949 82219.39 -29.4 -22.0 17.4 163842 1 3.533 117158 82219.39 -29.4 -22.0 17.4 163842 1 3.170 83424 82219.39 -29.4 -22.0 17.4 163842 The same thing happens to the ROIs on the RH (XYZ: 29.8 29.8 18.0). Best Wishes, Elijah -- Elijah Mak, Gates Scholar PhD Candidate | Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ 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 athttp://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. -- Elijah Mak, Gates Scholar PhD Candidate | Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ
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