Thank you Martin.

I created a minimal longitudinal table (fsid, sid-base, age, and years). Years is either 0 (timepoint 1) or 0.1 (timepooint2). I ran mri_slopes using this table, and made the cross table. I load qdec using the cross table, and have 2 continuous variables (years and age). I try to run an analysis using long.thickness-rate as the measure, with years as the covariate, and I keep getting an error screen "Error in Analyze: command failed: mri_glmfit --y ...."

If I use age as the covariate, the analysis works and I find no signficant differences (i.e. no relationship between thickness differences and age). Is there a way I can simply see if there are any thickness differences without using any covariates (so look at any areas of significant difference in thickness-rate) while correcting for multiple comparisons using fdr?

Thank you all your help.

Best wishes,

Sal

On Wed, Jul 9, 2014 at 6:13 AM, Martin Reuter <mreuter@nmr.mgh.harvard.edu> wrote:

Hi Sal,

it looks like you have everything together then. You can run your QDEC analysis on the long.thickness-rate (or one of the percent change files) to see where the rate is significantly different from zero. Negative rate means thickness decrease.

You could also use glmfit with the one sample group mean (-osgm) to test the same thing. There is a tutorial about that and also about multiple comparison correction.

After you create your within subject rate (or percent change) files. The whole thing turns into a simple cross-sectional analysis (as if you are analyzing thickness in a cross sectional design). Instead of thickness you now look at the 'change of thickness'. If you are unsure how to use qdec or glmfit, look at those tutorials first.

Best, Martin

On Jul 8, 2014, at 11:19 PM, Salil Soman <salsoman@stanford.edu> wrote:

Hi,

I have been following the tutorial from here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial

and here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel

And I believe I am running into problems with my GLM design.

I have a set of subjects with 2 time points each (all about 0.1 years apart).

All I wish to do is see what areas are significantly changed in volume, after correcting for multiple comparisons (fdr or montecarlo).

Could anyone suggest how I should setup the Design in QDEC?. I have included years and age in my cross.qdec.table.dat file (made from my long.qdec.table.dat file as described the tutorial, and have the measures of long.thickness-avg, long.thickness-rate, long.thickness-pc1 and long.thickness-spc avaialble (again from the tutorial).

Any advice would be greatly appreciated.

Sal

---------------------------------

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:

mreuter@nmr.mgh.harvard.edu

reuter@mit.edu

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Salil Soman, MD, MS

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