Hi Dr. Greve, Thanks for your reply.
Could you please confirm once recon-all -all is done, following steps are correct to get cortical thickness, volume and area stats using Yeo atlas: (1). Use "-sval-annot" option to transfer annotation (Ref. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-July/039348.html ) mri_surf2surf --srcsubject fsaverage --trgsubject XYZ --hemi lh --sval-annot $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7Networks_N1000.annot (2). Use "sval" option to transfer confidence map. (Ref. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-July/039348.html) mri_surf2surf --srcsubject fsaverage --trgsubject XYZ --hemi lh --sval $FREESURFER_HOME/subjects/fsaverage/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz --tval $SUBJECTS_DIR/$s/label/lh.Yeo2011_7NetworksConfidence_N1000.mgz (3). mris_anatomical_stats -a subjid/label/lh.aparc.annot -b subjid lh (4). aparcstats2table --subjectsfile SubIDs.txt --hemi lh --meas thickness -t LH_Thickness.txt Thanks. On Wed, Dec 14, 2016 at 4:34 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > You will need to create the yeo parcellation for each subject as well as > run mris_anatomical_stats to create the stats file, then run > aparcstats2table specifying the new stats file. Look in the > recon-all.log file to see how to call mris_anatomical_stats > > > On 12/14/2016 03:56 PM, Martin Juneja wrote: > > Hi, > > > > I would like to use aparcstats2table command. By default, it uses > > Killiany/Desikan parcellation atlas. But I would like to use atlas by > > Yeo and colleagues > > (https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation_Yeo2011 > ). > > > > Could you please let me know how can I use this atlas instead of > > default --parc and what would be the aparcstats2table command for this? > > > > Thanks. > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@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/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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. > >
_______________________________________________ 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.
