On 04/15/2014 10:34 PM, Pedro Rosa wrote: > Hi, Doug. > Thanks a lot! > The command would look like this: mri_glmfit-sim --glmdir > lh.thickness.Sch.glmdir --sim mc-z 10000 2 teste --sim-sign abs > --overwrite --cache 1.3 abs > It takes only a few seconds to run. The command is fine, but remove --sim mc-z 10000 2 teste. This tells it to do the simulation, which you don't need to do. It is overridden by the --cache flag. If they had occurred in the other order, you would be waiting days for the simulation to run. > I have a few questions about how to run it: > 1) How the single entry for each subject look like in the FSGD file? I'm not sure what you mean. Have you looked at the examples on the wiki? > > 2) How to define the voxel/vertex-wise used to define clusters (after > —sim, -log10( p)), and the voxel-wise threshold for the —cache option? > What is the difference between them? They are the same doug > > Thanks again, > Pedro Rosa. > > On Monday, April 14, 2014 at 3:29 PM, Douglas N Greve wrote: > >> >> 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> >>>>>>>> <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> >>>>>>>> <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> >>>>>>>> <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> >>>>>>>> <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> >>>>>>>> <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> >>>>>>> <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> >>>>>>> <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> >>>>>>> <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> >>>>>> <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> >>>>> <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> >>> 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 > 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
