On Thu, Jun 6, 2013 at 10:14 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

I think when you smooth it that much strange things happen. Try just one smoothing of 15mm.

On 06/06/2013 03:36 AM, Joshua deSouza wrote:

Hi Doug,

I did not specify anything in the mris_preproc, so it would be using the unsmoothed data. I only specify smoothing during the mri_surf2surf, which is 15 and then run glmfit. So what could be the reasons why i'm getting a residual fwhm of 47?

Regards,

Joshua

On Thu, Jun 6, 2013 at 12:16 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

Unless you specify otherwise, mris_preproc will use unsmoothed
data. If you then smooth it with mri_surf2surf and run run
mri_glmfit with --fwhm then you will be smoothing it twice.
doug

On 06/04/2013 09:49 PM, Joshua deSouza wrote:

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.com <mailto:desouzajoshua00@gmail.com>
<mailto:desouzajoshua00@gmail.com

<mailto:desouzajoshua00@gmail.com>>> wrote:

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.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu

<mailto:greve@nmr.mgh.harvard.edu>>> wrote:

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
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu

<mailto: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
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu

<mailto: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
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu

<mailto: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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Phone Number: 617-724-2358
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