Hi Martin,


Thank you that makes sense now.


I don't seem to be able to read a file into matlab containing hippocampal subfield volumes instead of the standard aseg using fast_ldtable. I haven't changed anything other than substituting hippocampal volume for dentate gyrus volumes. So the file consists of columns fsid, fsid-base, weeks, group, left_GC-ML-DG, right_GC-ML-DG, EstimatedICV. 276 rows.


The error I am getting in matlab is:


'Subscripted assignment dimension mismatch.


Error in fast_ldtable (line 84)

            tbl(nthrow-1,nthcol-1) = sscanf(char(s(nth)),'%f'); '


Do you have any idea what the problem is?


Thanks,


Amanda

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Martin Reuter <mreuter@nmr.mgh.harvard.edu>
Sent: 03 August 2017 08:15:29
To: Freesurfer support list
Subject: Re: [Freesurfer] Univariate Linear Mixed Effects
 
Hi Amanda,

the C matrix below has 14 columns ( 3 + 5 + 6 ). 

To find out what hypothesis are tested, look at the corresponding columns. 
column 4 for example is the MCIs slope delta with respect to controls (so slope difference MCIs and CN)
the next test is slope difference between MCIs and MCIc
and finally slope difference between MCIc and AD.

Your test 0 0 0 1 similarly tests slope difference between your two groups. And yes, the remaining columns would be control variables .

Best, Martin


On 31. Jul 2017, at 13:38, Worker, Amanda <amanda.worker@kcl.ac.uk> wrote:

Hi there,

I am currently working through the linear mixed effects example for hippocampal volume on the wiki and I can't quite get my head around how the contrast matrix is set up. 

In the example, the design matrix has 14 columns but the contrast matrix only seems to have 5 (below), could you explain why that is please? And also what hypotheses these three different contrasts are testing?

C = [zeros(3,3) [1 0 0 0 0; -1 0 1 0 0; 0 0 -1 0 1] zeros(3,6)];

At the moment I have a simple design with two groups, 4-5 time points so I have a design matrix with 4 columns (intercept, weeks, group, group*time) and the contrast I am using is [0 0 0 1] to test the interaction term. If I were to add covariates such as age and gender would I simply add two more columns to my design matrix and contrast to look like this...[0 0 0 1 0 0]?

Thanks in advance for your help.

Amanda
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "emea01.safelinks.protection.outlook.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer