Hi Anna, the matlab tools don't know. They only look at the other co-variates that you might want to include into your study (the fsid-base for grouping, the time variable and others from the table). The stack of thickness maps needs to be in the same order as the rows in the qdec table. That is why it is a good idea to use the same table to assemble the stack (and for that you'd use the -long-qdec flag and it uses the .long.base file names).
Best, Martin On Jun 24, 2014, at 5:23 PM, Anna Jonsson <ajonsso...@gmail.com> wrote: > Thank you. I just another question about the fsid groupings for the qdec > table for lme. If in the qdec I specify only the fisid (eg nt the > longitudinally processed subject with XX.long), and the XX.longs are in a > different folder, than how when I do the matlab lme tools does freesurfer > know to use the XXX.long scans? This is confusing me. > > Thanks for help,. > > Regards Anna > > > On Tue, Jun 24, 2014 at 11:26 AM, Martin Reuter <mreu...@nmr.mgh.harvard.edu> > wrote: > Hi Anna > I am not a statistician, but I would not control for duration separately, but > rather use the time variable for that. > It does not need to be in years (can be days out months). > Measures closer in time are more correlated than measures further apart. Lme > makes use of that information through the time variable. > Best Martin > Best Martin > > Sent via my smartphone, please excuse brevity. > > -------- Original message -------- > From: Anna Jonsson > Date:06/24/2014 11:52 AM (GMT+01:00) > To: Martin Reuter > Cc: Freesurfer support list > Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table > > thank you. and one other question; rather than putting years as the time > variable, can i do time 1 (for baseline) and 2 (for follow-up), and jsut > control for time between scans instead? > > > On Fri, Jun 13, 2014 at 5:42 PM, Martin Reuter <mreu...@nmr.mgh.harvard.edu> > wrote: > Hi Anna, whenever it says qdec-long the table is in qdec format (with a > fsid-base as second column. It would then use the longitudinally processed > results, which is what you want , both for lme and 2 stage model. > Best Martin > > > Sent via my smartphone, please excuse brevity. > > -------- Original message -------- > From: Anna Jonsson > Date:06/09/2014 3:47 PM (GMT+01:00) > To: Freesurfer support list > Subject: Re: [Freesurfer] free-surfer longitudinal Qdec table > > Hi, sorry for more questions, but i have a few. When running the first step > of the lme implemented tools, doing the command mris_preproc --qdec-long > qdec.table.dat --target study_average --hemi lh --meas thickness --out > lh.thickness.mgh (assembles your thickness data into a single > lh.thickness.mgh file), am I correct that this just needs to be a "normal" > cross-sectional qdec table that free surfer subsequently makes into long > format by --qdec-long option? so the lnogitudinal qdec table is only used in > the two stage modell? This too just uses the cross-sectionally derived scans? > Im confused where the .long runs become used? > > thank you and kind wishes > > > On Wed, Jun 4, 2014 at 5:01 PM, Martin Reuter <mreu...@nmr.mgh.harvard.edu> > wrote: > Hi Anna, > Fsid is the cross sectionall name without the .long. > Best martin > > > Sent via my smartphone, please excuse brevity. > > > -------- Original message -------- > From: Anna Jonsson > Date:06/04/2014 7:22 AM (GMT-05:00) > To: Freesurfer support list > Subject: [Freesurfer] free-surfer longitudinal Qdec table > > Hi, > > I would like to make my freesurfer longitudinal qdec table for the to use in > the lme matlab tools. However, does the fsid need to refer to the > longitidunally derived subject; eg XXX.long, or the cross-sectionally derived > subject, eg XXX. Im not sure based on the specification online. > Kind Regards > > Anna > > _______________________________________________ > 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. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu
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