For #1, Donald is right about FS -- you have to exclude the subject. For #2, you can use mri_concat with the --conjunct option (using sig or t or z maps as input).
the Conjunction option takes the min of the abs across frames at each voxel. The output value at the voxel is the min, including the true sign of the min. Eg, if the two frames are: +2.1 and +3.4 --> +2.1 -2.1 and -3.4 --> -2.1 +2.1 and -3.4 --> +2.1 -2.1 and +3.4 --> -2.1 See: Nichols, Brett,Andersson, Wager, and Poline NeuroImage, Volume 25, Issue 3, 15 April 2005, 653-660. doug MCLAREN, Donald wrote: > See inline responses.On Wed, Aug 24, 2011 at 7:35 AM, Tetiana Dadakova > <tetian...@gmail.com <mailto:tetian...@gmail.com>> wrote: > > Dear FS experts, > > I have two questions: > > 1. In qdec.table.dat file I am specifying several continuous factors, > e.g factor1 and factor2. For some subjects factor2 is missing, > therefore I leave empty space in those cells. When I load a > qdec.table.dat into qdec, the whole line of the subject with missing > factor2 is omitted. > I was wondering if I can make some input into the empty cell, so that > qdec recognizes that for this subject the value is missing only for > factor2, and the value for factor1 is present. > > > I'm not sure about Freesurfer, but in all my work with neuroimaging > data across platforms, missing data in X requires that the subject to > be excluded. The reason is the Y=X1*B+X2*B. Since you don't know X2, > you can't find predicted Y and thus you can't find the error > associated with that subject. Programs that all allow you to keep the > subject often impute the value of the missing data to get the full X > matrix or do not use the General Linear Model to find the solution. > The GLM approach inverts the X matrix and you can't invert a matrix > with an empty cell, as far as I know. > > > > 2. Is it possible to do conjunction analysis in FreeSurfer, I mean > looking at common differences in two groups as compared to the third > group? > > > When I do conjunctions, I use a logical AND. There are other ways, but > there are statistical issues. The logical AND will show where group A > > group C and where group B > group C. > To do this, I load the thresholded surfaces into matlab, make them > both binary, multiply one of them by 2, then add the two datasets > together. Then write the data back out to the surface. The new values > will be 0 for no difference in either group, 1 or 2 for a difference > in one of the group comparison, 3 where both groups are different from > the third. > > > > > Thank you for your time and help, > Tanja. > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > Best Regards, Donald McLaren > ================= > D.G. McLaren, Ph.D. > Postdoctoral Research Fellow, GRECC, Bedford VA > Research Fellow, Department of Neurology, Massachusetts General > Hospital and > Harvard Medical School > Office: (773) 406-2464 > ===================== > This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED > HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is > intended only for the use of the individual or entity named above. If the > reader of the e-mail is not the intended recipient or the employee or > agent > responsible for delivering it to the intended recipient, you are hereby > notified that you are in possession of confidential and privileged > information. Any unauthorized use, disclosure, copying or the taking > of any > action in reliance on the contents of this information is strictly > prohibited and may be unlawful. If you have received this e-mail > unintentionally, please immediately notify the sender via telephone at > (773) > 406-2464 or email. > ------------------------------------------------------------------------ > > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
