Hey Doug, thanks again! That means, I would do something like:
1.) construct longitudinal qdec table - only use fsid, fsid-base, and years/age columns - substract the average age of the one-time point subjects from years/age value for every subject at every time point 2.) run long_mris_slopes - use the --do-avg flag? 3.) concatenate the output files from 2) and the maps from the one-time point subjects with mris_preproc - use --is flag to select maps by specifying full path 4.) run mri_glmfit - use --osgm flag for one-sample group mean 5.) replace sig.mgz file with the one from LME analysis and run mri_glmfit-sim Is that correct? (especially, is using --do-avg what you meant by taking the offset) Thanks, Janosch Am 03.03.2015 um 08:32 schrieb Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > > I don't know, esp since it is an approximation to begin with. An alternative > is to take the offsets from your multi-time-point subjects and the single > maps from your subjects with one time point and run that through the > one-sample-group-mean (--osgm in mri_glmfit). If you go this route, then you > should subtract the mean age of the one time-point subjects from the age of > the multi-time point subjects before the 1st stage of analysis. > > doug > > > On 03/02/2015 07:25 PM, Janosch Linkersdörfer wrote: >> Hi Doug, >> >> thank you very much for your answer! >> >> Am 02.03.2015 um 11:30 schrieb Douglas N Greve <gr...@nmr.mgh.harvard.edu>: >> >>> You would do the long analysis using a random effects analysis. >> OK, so basically do 2-stage modeling >> (https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), right? >> >>> For each subject you can get a slope (this won't work if the subject only >>> has 1 time point), then concatenate the slopes into a file and run >>> mri_glmfit, then follow the procedures from the archive email you reference. >> One quarter of my subjects only has one measurement time point. Can I still >> use this method (which would only consider the 3/4 of the subjects) to >> correct clusters found in the whole group? Or would it only be valid for >> correcting clusters from an LME model for the reduced group? >> >> Thanks, >> >> Janosch >> >>> doug >>> >>> On 02/24/2015 08:35 PM, Janosch Linkersdörfer wrote: >>>> Hi Doug and others, >>>> >>>> I would like apply (Monte Carlo simulation) cluster correction (as opposed >>>> to the implemented vertex-wise FDR correction) on the results from a >>>> longitudinal study I analyzed using the LME toolbox. The design is >>>> unbalanced (different number of time points, from 1 to 4, per subject). >>>> >>>> In this thread >>>> (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35367.html) >>>> you, Doug, suggested, if I understand correctly: >>>> >>>> - concatenating the images using `mris_preproc --paired-diff` >>>> - smooth with the same kernel size as used in the lme analysis >>>> - running `mri_glmfit` on them with an fsgd file that uses the same >>>> covariates and the same contrast (excluding the interaction term with >>>> time) as used in the lme analysis >>>> - overwriting sig.mgh with the one from the lme analysis >>>> - running `mri_glmfit-sim --cache` >>>> >>>> How would I extend this to my case where I don't have pairwise images, but >>>> 1 image for some participants, for others up to 4? >>>> >>>> Thanks a lot, >>>> >>>> Janosch >>>> >>>> >>>> >>>> >>> -- >>> 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/ >>> >>> >>> >>> 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. >>> >> >> > > -- > 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
