On May 29, 2013, at 11:40 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote:
> Hi Joe, > > On 05/29/2013 01:00 AM, Joseph Dien wrote: >> I need to extract the beta weights from a cluster identified with >> FS-Fast in order to compute percentage signal change. >> >> 1) I see a file called beta.nii.gz that appears to have the beta >> weight information. It has a four dimensional structure and the >> fourth dimension appears to be the beta weights. Is there an index >> somewhere as to which beta weight is which? Or if not, how are they >> organized? > For the first level analysis, the first N beta weights correspond to the > N conditions in the paradigm file. The rest are nuisance variables. >> Ah, very good! In order to compute the percent signal change statistic (I'm following the MarsBaR approach: http://marsbar.sourceforge.net/faq.html#how-is-the-percent-signal-change-calculated) I'm also going to need the beta weights for the session mean regressors. How are the nuisance regressors organized? >> 2) In order to extract the cluster, it looks like I would >> use mri_label2vol to convert cache.th20.neg.sig.ocn.annot into a >> volume where the voxels are tagged with the number of the >> corresponding cluster. > Is that from a group analysis? >> Yes, that's right. >> I could then use that to generate masks to extract the information I >> need for each cluster from beta.nii.gz. > If this is from a group analysis, then there should already be a file > there (something.y.ocn.dat) that has a value for each subject in the > rows and a value for each cluster in the columns. >> I see it. Are these values already scaled as percent signal change? If so, that would be wonderful! :) >> Is that correct? >> >> 3) The final information that I would need is the canonical hrf shape >> generated by FSFAST for a single event. I guess I could generate that >> by setting up a dummy analysis run with a single event of the desired >> duration and then look in the X variable in the resulting X.mat file? > try this > plot(X.runflac(1).flac.ev(2).tirf, X.runflac(1).flac.ev(2).Xirf) >> Perfect! :) >> Sorry for all the questions! >> >> Joe >> >> >> >> >> -------------------------------------------------------------------------------- >> >> Joseph Dien, >> Senior Research Scientist >> University of Maryland >> >> E-mail: jdie...@mac.com <mailto:jdie...@mac.com> >> Phone: 301-226-8848 >> Fax: 301-226-8811 >> http://joedien.com// >> >> >> >> >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> 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. > -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdie...@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com//
_______________________________________________ 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.
