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.fwhm15/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 > <mailto: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 >> <mailto: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.fwhm15/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 >> <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.st >> <http://lh.testretest.thickness-pc1.st/>ack.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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <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 >> <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 > <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. > >
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