External Email - Use Caution
Hi,
I suppose what we are seeing in the top row of your figure are Freesurfer
labels, right? I.e. you probably used the '--olab' argument with the
'mri_surfcluster' command, and are loading each cluster from a different label
file?
If my speculation is correct, then what you observe could be due to the
'threshold' setting in freeview, i.e. this little box just below the label box
in the left part of the GUI.
This threshold is by default set to zero, but lowering it to some sufficiently
negative value (i.e. the minimum value in the 'sig' map) should also display
those regions that seem to be missing at the moment.
At least this is what I observed when I tried to reproduce your observation,
i.e. I could create (and reverse by setting another threshold) similar
'cut-outs' in the cluster maps.
In addition, you could also load the ouput files that are produced by the
'--o', '--ocn', or '--oannot' arguments of the 'mri_surfcluster' command. I
would guess that they don't show this pattern of missing areas.
Hope this helps,
Kersten
On Di, 2019-09-03 at 14:00 +1000, Bronwyn Overs wrote:
External Email - Use Caution
Dear Freesurfer mailing list,
I am trying to get to the bottom of a discrepancy between two surface based
images generated from the output of an LME analysis. The surfaces in row 1 of
the attached image were generated by loading the four FDR significant clusters
that were >100mm^2 in the cluster summary file. The surfaces in row 2 of the
attached image were generated by loading the significance map generated for the
same fixed effect (saved from the LME), and thresholding at the FDR corrected
p-value. The question I have is why are there such large swatches of the
cortical surface in the row 2 images that are labelled as log10 p = 5, when
they are not included in the most significant and largest clusters that were
found in the cluster summary file?
Kind regards,
Bronwyn Overs
Research Assistant
[cid:1567613630.3700.24.camel@dzne.de]
Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
M 0411 308 769 T +61 2 9399 1725
neura.edu.au <http://neura.edu.au/>
Twitter<https://twitter.com/neuraustralia> |
Facebook<https://www.facebook.com/NeuroscienceResearchAustralia> |
Subscribe<http://www.neura.edu.au/help-research/subscribe>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
