mris_preproc might work. You could also use mri_concat (mris_preproc is a front end for mri_concat)
On 03/03/2015 06:19 PM, Janosch Linkersdörfer wrote: > > 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/ >> > > -- 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
