Hi Martin, Thanks a lot. So it is uncorrected. Can one use the following cmd to do multiple comparison correction?
mri_glmfit-sim \ --glmdir lh.testretest.thickness-pc1.fwhm15 \ --cache 4 neg \ --cwp 0.05\ --2spaces I tried to run above cmd, it shows ERROR: thresh = 4,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 done Not sure if there is a bug or if my input is wrong. Any suggestions is appreciated! Best, Jahanvi On Thu, May 18, 2017 at 9:46 AM, Martin Reuter <mreu...@nmr.mgh.harvard.edu> wrote: > Hi Jahanvi, > > there should be a way to display the bar, but I don’t know how (others > will know)! > > sig is not FDR corrected. > > Best, Martin > > On 18 May 2017, at 08:56, jahanvi patel <jahanvipatel...@gmail.com> wrote: > > Hi Martin, > > Thanks a lot for the reply. Is there a way to display the bar in effect > size? > And is this sig.mgh already statistically corrected? (FDR?) > > Best, > Jahanvi > > On Thu, May 18, 2017 at 1:55 AM, Martin Reuter < > mreu...@nmr.mgh.harvard.edu> wrote: > >> Hi Jahanvi, >> >> I think red is positive (some people invert the colors, then >> red=hot=dangerous ). But I think default is blue negative, red positive, so >> there is an average increase in thickness. You should also look at the >> effect size (gamma). >> The p -values are in log 10 space, so 2 = 0.01 and 5 = 0.00001 >> >> Best, Martin >> >> On 17 May 2017, at 22:17, jahanvi patel <jahanvipatel...@gmail.com> >> wrote: >> >> Hi Martin, >> >> Thanks a lot. It had worked nicely. >> I got one question about this following cmd >> >> tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1.fw >> hm15/osgm/sig.mgh >> >> I got a red to yellow sig.mgh, does it mean I got a increased percent >> thickness change (pc1)? and the color bar showing 2 to 5 means? >> >> Best, >> Jahanvi >> >> >> >> On Sun, May 14, 2017 at 10:11 PM, Martin Reuter < >> mreu...@nmr.mgh.harvard.edu> wrote: >> >>> Hi Jahanvi, >>> >>> 1. yes, you need to create this table to then perform the stats >>> 2. no, the format is as I described it below >>> fsid fsid-base >>> tp1_subA templatesubA >>> tp2_subA templatesubA >>> tp1_subB templatesubB >>> tp2_subB templatesubB >>> >>> this is assuming that you called your base templatesubA and templatesubB >>> for the two subjects. It will automatically look in the >>> tp1_subA.long.templatesubA etc. directories. >>> >>> Best, Martin >>> >>> On 12 May 2017, at 16:55, jahanvi patel <jahanvipatel...@gmail.com> >>> wrote: >>> >>> >>> Hi Martin, >>> >>> Do you mean by creating this long.testretest.qdec file, one can then >>> perform the stats for the longitudinal2StageModel? >>> >>> So for a 2 timepoints analysis, eg. TP1 & TP2. >>> the long.testretest.qdec will be looking like this ? >>> >>> >>> fsid fsid-base >>> >>> tp1_subA.long.TemplatesubA tp2_subA.long.TemplatesubA >>> tp1_subB.long.TemplatesubB tp2_subB.long.TemplatesubB >>> tp1_subC.long.TemplatesubC tp2_subC.long.TemplatesubC >>> >>> . >>> . >>> . >>> >>> >>> Thanks, >>> >>> Jahanvi >>> >>> >>> >>> tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1.fw >>> hm15/osgm/sig.mgh >>> >>> >>> Hi Jahanvi, >>>> >>>> long.testretest.qdec is a qdec table in the longitudional format (with >>>> the fsid-base as the second column). >>>> >>>> For test-retest (e.g. same session with subject removal), you usually >>>> don't need a time column, that is why --generic-time is specified. the qdec >>>> table would just look like >>>> >>>> fsid fsid-base >>>> >>>> me me_test >>>> >>>> me me_retest >>>> >>>> you you_test >>>> >>>> you you_retest >>>> >>>> ... >>>> >>>> >>>> Best, Martin >>>> >>>> >>>> On 05/08/2017 04:10 PM, jahanvi patel wrote: >>>> Hello list, >>>> >>>> I have a simple question about the LongitudinalTwoStageModel tutorials >>>> on freesurfer website. >>>> >>>> It is from this link >>>> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel >>>> >>>> >>>> long_mris_slopes --qdec long.testretest.qdec \ >>>> --meas thickness \ >>>> --hemi lh \ >>>> --sd $SUBJECTS_DIR \ >>>> --do-pc1 --do-label \ >>>> --generic-time \ >>>> --fwhm 15 \ >>>> --qcache fsaverage \ >>>> --stack-pc1 lh.testretest.thickness-pc1.stack.mgh \ >>>> --isec-labels lh.testretest.fsaverage.cortex.label >>>> >>>> My question is, what is the content of long.testretest.qdec ? >>>> I understood till 1st stage was done, we got only one file which is >>>> long.qdec.table.dat. >>>> >>>> Could anyone help to clarify my question? >>>> >>>> Thanks a lot >>>> Jahanvi >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> 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 >>> >>> >>> >>> 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 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.
