On 02/29/2016 02:38 AM, Bittner, Nora wrote: > > Dear FreeSurfer Experts, > > Sorry for reposting this massage again, but I still have two > questions, which you can hopefully answer to: > > 1) > > I calculated several analyses with LGI as my dependent variable, > resulting in several significant clusters. > > Now, I would like to extract the individual LGI value at the *maximum > vertex* of each significant cluster to plot it against my experimental > variables (instead of working with the mean LGI values of the clusters). > > What I tried so far is to use mri_segstats to extract the LGI at the > maximum vertex: > > mri_segstats --i $SUBJECTS_DIR/qdec/glm/y.mgh --crs vertexno 84367 0 0 > --avgwf vertexno84367.dat > > where y.mgh is my input file from the glm and vertexno 84367 is the > maximum vertex of the cluster as reported in the cluster.summary-file. > > I found the command in the FS helpline documentation > (https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42655.html), > but regrettably > <http://dict.leo.org/ende/index_en.html#/search=regrettably&searchLoc=0&resultOrder=basic&multiwordShowSingle=on> > > I get the following error message: > “ERROR: Option –-crs unkown” > In the fswiki I also couldn´t find the “mri_segstats - - crs option” > in the user description. > Is there any other option or argument I can use in mri_segstats (or in > any other command) to extract the LGI value per person at the given > vertex? Remember, you can always run commands with --help to get more info. If you run this command with --help, you will see: --vox C R S replace seg with all 0s except at CRS
So use --vox, not --crs. > > 2) > > I would like to calculate effect sizes of my results. Therefore I used > fscalc: > > fscalc $SUBJECTS_DIR/qdec/glm/contrast/gamma.mgh div > $SUBJECTS_DIR/qdec/glm/rstd.mgh -o $SUBJECTS_DIR/qdec/ > glm/contrast/effectsize.mgh > This worked fine and resulted in a surface overlay displaying the > effect sizes. Now, I would like to extract these effect sizes in > 'table' format. I tried to use mri-segstats: > > mri_segstats* --i effectsize.mgh --annot fsaverage lh aparc --avgwf > effectsize.dat > > I am not sure, if this gives me the correct results. Is this the right > command? > > I would really appreciate > <http://dict.leo.org/ende/index_en.html#/search=appreciate&searchLoc=0&resultOrder=basic&multiwordShowSingle=on> > > your help. > Yes, that will give you the effect size averaged over each annotation > > Thank you in advance, > > Nora > > > > ------------------------------------------------------------------------------------------------ > ------------------------------------------------------------------------------------------------ > Forschungszentrum Juelich GmbH > 52425 Juelich > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher > Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > ------------------------------------------------------------------------------------------------ > ------------------------------------------------------------------------------------------------ > > > > _______________________________________________ > 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.
