It is probably better to work with the y.mgh file that qdec produces. It is in fsaverage space. If you create an ocn file with mri_surfcluster, you can feed that as the --seg to mri_segstats (along with --i y.mgh), spec the output with --avgwf to get a matrix of nsubjects by nclusters (make sure to also include --exludeid 0)
On 01/23/2017 08:00 PM, Katherine Damme wrote: > Thank you so much! > > This got me to the stage of having separate labels for each > significant cluster, but I would like to extract the values from each > subject to look at the raw data. > > Do I have to use mri_label2label to move the label into each > individual's space? > > Can I use aparcstats2table to get a table of the individual values of > the label? > (It seems that this is set up for the segmentation data) > > Thank you again! > > > On Mon, Jan 23, 2017 at 11:44 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Try mri_surfcluster. Run it with --help to get usage. You can set the > threshold with --fdr. Make sure to use the --mask option passing > it the > mask.mgh from the qdec output > > > On 01/22/2017 07:56 PM, Katherine Damme wrote: > > Hello Everyone, > > > > Is there a way to extract the significant clusters as masks from > > significant group comparisons using qdec? > > > > All I can seem to find is mri_glmfit-sim which doesn't quite > > replicate the QDEC FDR 0.05 output and doesn't seem to make anything > > that I could extract as a label, or hand drawing an ROI. > > > > I am working with a longitudinal model of cortical thickness, and > > would like to extract the average thickness of each significant > > cluster to understand the change in thickness. > > > > Thank you. > > > > Kate Damme > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > <https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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. > > -- 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
