Hi Martin, Thanks for your instructions. In my analysis when we look at Two Stage Model results within our control group , we see increase in thickness (thickening) more than decrease (thinning), where we expect to see the thinning effect. Is there any explanation for this? I have 19 controls with 2 to 3 years difference between tp1 and tp2.
Best regards, Amirhossein Manzouri On Mon, Feb 23, 2015 at 5:25 PM, Martin Reuter <mreu...@nmr.mgh.harvard.edu> wrote: > Hi, > > yes, the first is to stack all the data into a single file (on your study > average, usually that is fsaverage). The second steps smoothes the data. > You can use different smoothing levels, depending on your data. Usually 10 > or 15 is a good number. > > The data will automatically be taken from the sub1t1.long.tempsub1 etc > directories (this is signaled by the --qdec-long flag. The qdec table needs > to be in the longitudinal format, that means the first column is the > subject id (sub1-t1) the second column the base name (tempsub1) column > headers are fsid fsid-base …. > usually the third column is time from baseline (in years), but can be any > time variable that you want to use in the LME. > > There is an example of the longitudinal qdec table here: > http://freesurfer.net/fswiki/LongitudinalTwoStageModel > > I'll probably add that to the lme page so it is easier to find. > > Best, Martin > > On Feb 23, 2015, at 4:54 AM, amirhossein manzouri <a.h.manzo...@gmail.com> > wrote: > > Hi and thanks Martin for your help, > I am trying to do mixed effect analysis, should I use the registered to > template data for this ( sub1-t1.long.tempsub1 and sub1-t2.long.tempsub1) > and how should the aded.table.dat look like? Do I need to run : > > mris_preproc --qdec-long qdec.table.dat --target study_average --hemi lh > --meas thickness --out lh.thickness.mgh > > mri_surf2surf --hemi lh --s study_average --sval lh.thickness.mgh --tval > lh.thickness_sm10.mgh --fwhm-trg 10 --cortex --noreshape > > > --------------------------------- > 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 > > 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. >
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