New subject: Cortical thickness

4 Jun 2013

      Hello Doug,
Each individuals subject data has already been smoothed by 5 10 15 20 and
25 through the qache function during the initial processing.
I'm a little confused now. I thought that the mri_preproc would use the
non-smoothed values of the subjects and create an mgh file. After which I
smooth the mgh file and then use mri_glmfit to analyse it according to the
contrasts.
If the above is not the case and the subject data has already been
smoothed, then what should I do if I wish my final mgh file to have a
smoothing value of 15 before doing a glmfit on it?
Thank you,
Joshua
On Wed, Jun 5, 2013 at 12:40 AM, Joshua deSouza
desouzajoshua00@gmail.comwrote:
...
Hello Doug,
Each individuals subject data has already been smoothed by 5 10 15 20 and
25 through the qache function during the initial processing.
I'm a little confused now. I thought that the mri_preproc would use the
non-smoothed values of the subjects and create an mgh file. After which I
smooth the mgh file and then use mri_glmfit to analyse it according to the
contrasts.
If the above is not the case and the subject data has already been
smoothed, then what should I do if I wish my final mgh file to have a
smoothing value of 15 before doing a glmfit on it?
Thank you,
Joshua
On Mon, Jun 3, 2013 at 11:13 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
...
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 <greve@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 <
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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Re: [Freesurfer] Cortical thickness