On 04/14/2014 10:35 AM, Pedro Rosa wrote: > Dear Doug and Jorge, > I tried what you suggested and I think it work, although I have some > concerns. > I am working with a longitudinal study with two time-points for all > subjects, three categorical variables (group, substance abuse / > dependence and gender) and three continuous variables (interval > between scans, age and medication intake). > I generated a contrast with intercept + 7 betas for the LME, ran it > without any problem and saved the sig.mgh using > fs_write_fstats(F_lhstats,mri,’sig.mgh’,’sig’). > For the mri_glmfit I entered the same output from mri_surf2surf I used > for the LME (smoothed at 10mm), but I did not know how exactly to > enter the categorical and continuous variables, or which contrast to use. I would do it as a paired-test (see the wiki). You may have to re-run mris_preproc with the --paired-diff flag, then smooth by 10mm. Use this as the input to mri_glmfit. Set up the FSGD with the categorical and continuous variables (note that the FSGD file will have only a single entry per subject). Create your contrasts and run mri_glmfit. Overwrite the sig.mgh with the one from LME. Then run mri_glmfit-sim with the --cache option (not permutation)
I don't know what your contrast of interest is, so I can't help you there. In the end, it does not matter because you are overwriting the sig map anyway. You just need a contrast as a place holder. doug > The commmand was: mri_glmfit —y pval.mgh —sim perm 10000 0.05 sch > > I just tested creating a matrix with 24 columns > (Nclasses*(Nvariables+1) as suggested for DODS). > Afterwards I ran the mri_glmfit-sim (mri_glmfit-sim --glmdir > Sch-glmdir --sim mc-full 5 2 teste --sim-sign abs, and it finished > apparently without errors. > I attached the logs for both mri_glmfit and mri_glmfit-sim. > > That said, I have the following questions: > > 1) What does the FWHM procedure does? > 2) How should I decide which contrast to test if the mri_glmfit does > not consider the longitudinal design? > 3) Will the mri_glmfit-sim consider only the FMHM output from > mri_glmfit and sig.mgh from the LME, or also other outputs from the > mri_glmfit? > 4) Does the FWHM rely only on the images, and not on variables and > contrasts? > > Thank you very much! > Pedro Rosa. > > On Monday, March 31, 2014 at 10:53 PM, Pedro Rosa wrote: > >> Thanks, Doug! >> Should I run the mri_preproc and and smooth the output using >> mri_surf2surf with, let’s say, 10mm, and than run the LME normally in >> MatLab? >> Would this be problematic with a different smoothing procedure in >> mri_glmfit? >> How will mri_glmfit deal with the longitudinal design? Does this >> matter, or the FWHM would only be estimated on a average image of all >> time-points for all subjects? >> Regards, >> Pedro Rosa. >> >> On Sunday, March 30, 2014 at 3:51 PM, Douglas Greve wrote: >> >>> >>> I think I would just run mri_glmfit on your data to get the proper >>> directly structure and estimate of FWHM, then copy the sig file from >>> the mixed fx analysis into the glmfit folder for one of the >>> contrasts. Then run mri_glmfit-sim. >>> >>> doug >>> >>> >>> On 3/29/14 10:29 AM, Pedro Rosa wrote: >>>> Dear Doug and Jorge, >>>> Thank you very much for your help. >>>> I found another message in the list >>>> (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-November/034649.html) >>>> >>>> in which you suggested a way of using MC in mri_glmfit-sim by >>>> creating “fake files”, which would not be read by the script. In >>>> this case, only the simulation would be run, and not the full >>>> statistics. The command would be something like this: >>>> - mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste >>>> --sim-sign abs >>>> I created a “fake” mri_glmfit.log, fwhm.dat and mask.mgh files as >>>> suggested by the older post. This would be fine, I believe, if only >>>> sig.mgh is read by the script. >>>> However, I get this message after running the command: >>>> >>>> [server:Long-T0-T2-Posproc/Vertex/Sch] pedrogomesrosa% >>>> mri_glmfit-sim --glmdir $SUBJECTS_DIR --sim mc-full 5 2 teste >>>> --sim-sign abs >>>> >>>> if: Expression Syntax. >>>> >>>> >>>> Is it possible to do what I am trying to do? Does the residual >>>> errors at each location included in the sig.mgh, and, if necessary, >>>> how to compute it into image FWHM? >>>> >>>> Regards, >>>> >>>> Pedro Rosa. >>>> >>>> On Friday, March 28, 2014 at 2:38 PM, Douglas N Greve wrote: >>>> >>>>> Jorge, do you output the FWHM? >>>>> doug >>>>> >>>>> On 03/27/2014 03:14 PM, jorge luis wrote: >>>>>> Hi Pedro >>>>>> >>>>>> Sorry, right now the only multiple comparisons corrections >>>>>> implemented >>>>>> in lme are the original Benjamini and Hochberg (1995) FDR procedure >>>>>> (lme_mass_FDR) and a more recent and powerful two-stage FDR >>>>>> procedure >>>>>> (lme_mass_FDR2): >>>>>> >>>>>> Benjamini, Y., Krieger, A.M., Yekutieli, D. (2006). Adaptive linear >>>>>> step-up procedures that control the false discovery rate. >>>>>> Biometrika, >>>>>> 93, 491-507. >>>>>> >>>>>> In my experience, this procedure is as powerful to detect effects in >>>>>> neuroimage data as alternative corrections with strong control of >>>>>> the >>>>>> family-wise error rate (FWE). However it would be great if we could >>>>>> use an implementation of any multiple comparisons correction with >>>>>> strong control of the FWE (MC, RFT, ect...) for lme (FDR procedures >>>>>> only provide weak control). The residual errors at each location >>>>>> required to compute an estimate of the image FWHM can be obtained >>>>>> from >>>>>> the lme output. But an actual FWHM estimate is not currently saved. >>>>>> >>>>>> Best >>>>>> -Jorge >>>>>> >>>>>> >>>>>> El Martes 25 de marzo de 2014 8:15, Pedro Rosa >>>>>> <pedrogomesr...@gmail.com <mailto:pedrogomesr...@gmail.com>> >>>>>> escribió: >>>>>> >>>>>> Dear Doug, >>>>>> Thank you very much! >>>>>> I will try what you suggested, although I am not sure if Jorge's >>>>>> stream outputs the FMHM, or if I would need to run the statistics >>>>>> from the beggining using in the terminal, and not in MatLab. >>>>>> Do you think Jorge could comment on this issue? >>>>>> Regards, >>>>>> Pedro Rosa. >>>>>> >>>>>> On Mar 24, 2014, at 12:44 PM, Douglas Greve >>>>>> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >>>>>> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >>>>>> >>>>>> >>>>>> In theory, it should be possible. I have not used Jorge's stream, >>>>>> so I >>>>>> don't know that much about it. Does it save an estimate of the >>>>>> FWHM? If >>>>>> so, then you can run mri_surfcluster passing it the p-value (ie, >>>>>> -log10(p)) map, the FWHM, the mask, and a voxel-wise threshold. >>>>>> This is >>>>>> what mri_glmfit-sim does, so you might check that script for >>>>>> mri_surfcluster command line options >>>>>> >>>>>> doug >>>>>> >>>>>> >>>>>> > On 3/22/14 11:03 PM, Pedro Rosa wrote: >>>>>> > Dear list, >>>>>> > I ran the recon-all and the Freesurfer 5.1 longitudinal pipeline >>>>>> in a structural MRI dataset and I would like to use Monte Carlo as >>>>>> the method for correction for multiple comparisons. However, the >>>>>> longitudinal LME tutorial includes only FDR correction >>>>>> (lme_mass_FDR2). >>>>>> > Is it possible to use Monte Carlo correction for longitudinal >>>>>> data? Can I input the outputs from MatLab (fstats = >>>>>> lme_mass_F(?h,CM): stats.F / pval / sgn / df) into mri_glmfit and >>>>>> then run Monte Carlo? >>>>>> > If not, do you have any other suggestions of how I use Monte >>>>>> Carlo in longitudinal analyses? >>>>>> > Thanks in advance, >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> <mailto: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. >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> <mailto: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 <mailto: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 >>>>> <http://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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu <mailto: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. >> > > > > > > > > _______________________________________________ > 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: 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
