Am 03.03.2015 um 14:42 schrieb Douglas N Greve <gr...@nmr.mgh.harvard.edu>:
> > Some of this Martin will have to comment on, but my comments below > > On 03/03/2015 12:35 PM, Janosch Linkersdörfer wrote: >> 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? > Yes, I think so >> >> 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 > What command are you talking about to do the concatenation? mris_preproc, I thought. Thanks for your help, Janosch > Otherwise sounds right. Make sure you use the average of the time points from > long_mris_slopes and not the slope. >> >> 4.) run mri_glmfit >> - use --osgm flag for one-sample group mean > Yes >> >> 5.) replace sig.mgz file with the one from LME analysis and run >> mri_glmfit-sim > Yes >> >> 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/ >>> >> >> > > -- > 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
