On May 29, 2013, at 11:40 AM, Douglas N Greve greve@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.
- 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-cal...) I'm also going to need the beta weights for the session mean regressors. How are the nuisance regressors organized?
- 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?
- 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: jdien07@mac.com mailto:jdien07@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 greve@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: jdien07@mac.com Phone: 301-226-8848 Fax: 301-226-8811 http://joedien.com//