Hi Joshua, when you add --fwhm 15 to the command line you are
instructing mri_glmfit to smooth by 15mm. Is this what you want? Or is
the data already smoothed?
doug
On 6/3/13 12:26 AM, Joshua deSouza wrote:
Hi Doug,
The command line is mri_glmfit --y lh.t.15.mgh --fsgd t.txt dods --C
t1.txt --surface fsaverage lh --cortex --fwhm 15 --glmdir lh.t.15.glmdir
I am doing a whole hemisphere analysis and am measuring cortical
thickness. I do not have my own mask but I have doubts about the mask
that has been produced because from previous studies, there has been
significant thinning in the area around the hippocampus and parts of
it are being left out in the mask, such as the para-hippocampal region.
Regards
Joshua
On Mon, Jun 3, 2013 at 10:54 AM, Douglas Greve
<gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
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
<gr...@nmr.mgh.harvard.edu <mailto:gr...@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
<gr...@nmr.mgh.harvard.edu
<mailto:gr...@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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