Hi Tudor, On 03/22/2013 05:19 PM, Tudor Popescu wrote: > Hello everyone, > > I created a qdec.table.dat for my design (a simple group analysis, > with gender as categorical factor and age as continuous factor), and > created a gender.levels file containing the values that are found in > qdec.table.dat, spellt in exactly the same way (all files attached). > However, when loading the file in QDEC, I get the error: > > /ERROR: Subject C01 has an invalid level 'controls' in the group column > INFO: If 'group' is a discrete factor, then create a file named > 'group.levels' containing the valid factor names one per line. > Error loading the data table. > / > > The strings under the fsid column (subject ID) correspond to those > that I used after the –subjid xxx, in my previous call to recon-all > (e.g. "C01, C02, M01, M02.."). The qdec.table.dat was created in Excel > and saved as a tab-delimited txt file. Replacing the tabs with > spaces/commas does not change the error message. What could be the > problem? It looks like you made the group.levels file on a windows system. There are hidden characters that cause qdec to fail. Try creating it from scratch on a linux system or run dos2unix on the file. > > > I also have a few more questions, if I may: > > - how much more accurate are the results of a QDEC analysis if an > average subject is computed from the subjects of the sample, with > make_average_subject, as opposed to using FS's default average > subject, fsaverage?
Accurate in what way? Changing the average subject in qdec just changes the gray scale curvature pattern. This will be a little more accurate if you use your subjects, but probably not much. It will change the stats a very small amount. Note that QDEC will not use a different registration even if you spec a new average subject. > > - the qdec.table.dat in the tutorial > <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis>contains > > more than just "demographical information", for instance it contains > the volumes of the left and right hippocampi; are these types of > informations normally brought in from previous analyses (that may have > been done in a package other than FS), or does one first have to > obtain any such relevant predictors in FreeSurfer, before starting the > QDEC analysis? They do not have to be. They are only there for convenience in case you have a hypothesis about them. > > - the QDEC tutorial seems to be for whole-brain analyses; the ROI > analysis tutorial > <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI> > mentions nothing of QDEC, however; can ROI analyses not also be done > in QDEC? No, not yet. > > - in the Group Analysis (non-QDEC) tutorial > <http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis>, > the design matrix (Xg.dat) is in the form MembershipF| > MembershipM|AgeF|AgeM, while the values in the contrast are said to > correspond to the 4 parameters (intercept for F,M; slope for F,M). > Either way, how can the contrast vector be interpreted to give the > correlation between thickness and age? Each column in the Xg.dat is matched with a linear parameter (intercept or slope). If you have [0 0 1 0], it means to ignore the parameters matched with 0s and just test the parameter matched with 1, in this case, the AgeF (and so slope) parameter. > > - in the same tutorial, why is the value 0 being given to the first > two elements in the matrix, when it should only be given to nuisance > variables? Effectively yes. They might only be "nuisance" for that particular contrast. For other contrasts they might be variables of interest. doug > > Many thanks in advance for any help! > Tudor > > > _______________________________________________ > 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 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.
