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>> 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>> 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>> 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>> 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:Freesurfer@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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