Sandra, what was your final command line? doug On 07/03/2013 06:28 AM, Sandra Preissler wrote: > Dear Doug, > > Thanks a lot for your advice. > > We followed the examples on the wiki > (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#AssembletheData.28mrispreproc.29) > > and tried to analyze our data as described. > We have a single group with two continuous covariates. Therefore we > created the freesurfer descriptor file (g1v2_I.fsgd) and three > contrast files (main.mtx; age.mtx; Amputationsdauer.mtx). The > preprocessing finished without error for both hemispheres. > > The following command line we used for the preprocessing: > mris_preproc --fsgd qdec/GLM/g1v2_I.fsgd --cache-in > long.thickness-avg.fwhm10.fsaverage --target fsaverage --hemi lh --out > lh.g1v2_I.thickness.10.mgh > > After this we tried the mri_glmfit for our longitudinal data. > Our command line was the following: > mri_glmfit --glmdir g1v2_I --y lh.g1v2_I.thickness.10.mgh --fsgd > qdec/GLM/g1v2_I.fsgd --C qdec/GLM/main.mtx --C qdec/GLM/age.mtx --C > qdec/GLM/Amputationsdauer.mtx > > We get the error message: > ERROR: you must use '--surface subject hemi' with surface data > > Therfore we tried to specify > > subject as fsaverage, > hemi as lh, > surface as thickness. > > Unfortunately, this did not work out and other alternative approaches > to solve this problem did not function as well. > > Do we have to create a subject descriptor file for our longitudinal > templates? > Or did we miss anything else? > We thought about creating the --X “design matrix file” for > longitudinal data, we found the instruction for between factors. But > this could not work for our data. > > Best regards > Sandra > > > > > -----Nachricht von gr...@nmr.mgh.harvard.edu -----Datum: Fri, 28 Jun > 2013 10:40:57 -0400 > Von: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > Betreff: Re: [Freesurfer] longitudinal analyses for one group > An: freesurfer@nmr.mgh.harvard.edu > > Hi Sandra, you cannot do the longitudinal statistical analysis in QDEC. > You will have to use mri_glmfit. Look at the FSGD examples on the wiki. > doug > > > > > > On 06/28/2013 03:28 AM, Sandra Preissler wrote: > > > [Zitattext verstecken] > Dear freesurfer experts, > > we want to do longitudinal analyses for two different time points in > only one group (We do not have a control group or different groups > within the intervention). So we did the longitudinal processing as > described in the tutorial > (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial#PreparingtheData-QCACHE). > > > Now we tried to investigate the results with Qdec. We wanted to test > whether the averaged change of thickness between pre-test and > post-test differs from zero. We had the experience that we could only > test the averaged thickness by choosing a discrete factor in Qdec. Our > Problem is that we don't have a control group. So we couldn't choose > the group variable as discrete factor. > It's an pre-post-design with only one group. > > Is it possible to investigate changes in thickness between pre-test > and post-test without choosing a factor? Or do we have to create a > group variable as discrete factor? > > Can you help us in fixing this problem? > > Thanks in advance! > > Sandra > > ---------------------------------------------------------------- > This message was sent through https://webmail.uni-jena.de > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ---------------------------------------------------------------- > This message was sent through https://webmail.uni-jena.de > >
-- 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.
