The residual FWHM is measured from the data itself. You apply a certain amount of smoothing, but there is already some smoothness to the data, so the final fwhm is a combination of what is already there and what you apply. A fwhm of 47 is huge and may indicate that something is wrong. What is the input? cortical thickness? Are you using your own mask or is this a whole hemisphere analysis?

doug





On 6/2/13 10:29 PM, Joshua deSouza wrote:
Hello Doug,

Thank you for your quick replies to my queries. Really appreciate it.

I have found the files containing the cortical thickness values. Thank you. I assume that the order in which they follow are based on the fsgd file and the cluster annotation numbers.

I was just slightly confused about the residual fwhm. I have already done a smoothing of 15 on the file and have recieved a residual value of 47, which I assume is extremely large. Since I'm finding out values for the entire cortex I cannot do a glmfit-sim as there are no fwhm cache values of 47. Could you please tell me what the residual values mean?  What do you recommend I do? Is there anything I can read up on to find out more about this? (Please pardon my questions if they seem a little trivial)

Thank you

Joshua

On Sun, Jun 2, 2013 at 11:33 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

This file is always created by mri_glmfit-sim. It might be named something different depending on your parameters (should always end in y.ocn.dat)
doug


On 6/2/13 3:57 AM, Joshua deSouza wrote:
Hi Doug,

This file that your saying, will be created after glmfit-sim is done using the cache function and a threshold of 1.3 and absolute ,with y being the fsgd file? Am I understanding this correctly?

Thank you

Joshua

On Sat, Jun 1, 2013 at 12:14 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
There should be a file called something like cache.th13.abs.y.ocn.dat.
This will have a column for each cluster and a row for each subject. The
value in the row will be the input for each subject.
doug

On 05/30/2013 11:21 PM, Joshua deSouza wrote:
> Hello everyone,
>
> Please pardon my rather simple question
>
> I have done a GLM fit anlysis and have obtained a file sig.mgh alonf
> with a few others after the analysis.As I know, I do not have to
> create ROIs in order to do this. I also understand that doing a
> multiple comparison analysis just compares the regions of importance
> and evaluates them giving the most resilient cluster depending on the
> threshold. So, this does not give a thickness estimate. I would like
> to know how do I get the cortical thickness values from the results?
> If so, can I do it after glmfit?
>
> And thanks Doug for your help in the other questions that I had prior
> to this!
>
> Thank you
>
>
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