Hi Doug,
Sorry I am not sure that I understand. Does the --y file contain all of
the values for each individuals subject, mapped to the fsaverage image?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au <http://neura.edu.au>
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On 20/04/2015 9:14 am, Douglas Greve wrote:
No, it gets the information from the stack of data used as the --y
input to mri_glmfit.
doug
On 4/19/15 7:05 PM, Bronwyn Overs wrote:
Hi all,
I am still a little confused as to how the individual values are
calculated for the significant clusters in the GLM model. Is the
cluster mapped backed on the individual brain and the mean thickness
for that region is printed out for each individual?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au <http://neura.edu.au>
Follow @neuraustralia on twitter
<https://twitter.com/neuraustralia>Follow NeuRA on facebook
<https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to
the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>
On 14/04/2015 9:29 am, Bronwyn Overs wrote:
Hi Doug,
Sorry which file should the mri_segstats command be in? Also, I am
still unclear on how the individual values in
cache.th13.abs.y.ocn.dat are calculated. Could you possibly explain
this?
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au <http://neura.edu.au>
Follow @neuraustralia on twitter
<https://twitter.com/neuraustralia>Follow NeuRA on facebook
<https://www.facebook.com/NeuroscienceResearchAustralia>Subscribe to
the NeuRA Magazine <http://www.neura.edu.au/help-research/subscribe>
On 13/04/2015 11:34 pm, Douglas Greve wrote:
I'm not sure what the problem is, but it occurs to me that
computing the mean over the cluster is probably not what should be
done. Instead, the total should be computed. In the header of that
file, there should be a command line for mri_segstats. Cut and
paste that into a shell and add --accumulate and see if the numbers
get more reasonable.
doug
On 4/6/15 9:48 PM, Bronwyn Overs wrote:
Dear Freesurfer Mailing List,
I have just run a GLM analysis using mri_glmfit with area as the
measure of interest. For each of my significant contrasts, I
extracted the mean area for each subjects from the corresponding
cache.th13.abs.y.ocn.dat file. I then plotted these values to
examine the nature of the interaction. In doing so I identified
three individuals who had extreme mean area values (up to 11 sd
from the average of the mean area) for many of the significant
clusters. For each of these individuals I cannot see any problems
with the freesurfer .mgz files or the cortical segmentation.
So my questions are:
1. Are extreme mean values for significant clusters in GLM a
problem? If so, do you have any idea what could be causing these
values if the scans appear to be well segmented?
2. If the significant clusters are calculated at a group level,
how are the individual mean values (in cache.th13.abs.y.ocn.dat)
generated?
--
Kind regards,
Bronwyn Overs
Research Assistant
Neuroscience Research Australia
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265
neura.edu.au <http://neura.edu.au>
Follow @neuraustralia on twitter
<https://twitter.com/neuraustralia>Follow NeuRA on facebook
<https://www.facebook.com/NeuroscienceResearchAustralia>
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