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 <greve@nmr.mgh.harvard.edu mailto:greve@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 greve@nmr.mgh.harvard.edu <mailto:greve@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.