External Email - Use Caution
Hi Bronwyn,
thanks for sending the files.
I've taken a look, and suggest that you leave out the '--thmax 5' argument from
your mri_surfcluster command. Then, it may still be necessary to set the label
threshold value in Freeview to a value below zero.
When I run the modified mri_surfcluster command with the example data you
provided, the created label resembled the mgh file, i.e. no cut-outs in regions
of high significance were present.
Best regards,
Kersten
On Di, 2019-10-15 at 11:03 +1100, Bronwyn Overs wrote:
External Email - Use Caution
Hi Kersten,
That would be very helpful thank you. What email address should I designate as
the recipient when using Freesurfer FileDrop?
Kind regards,
Bronwyn Overs
Research Assistant
[cid:1571816394.29396.7.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>
________________________________
From: "Kersten Diers, DZNE" <kersten.di...@dzne.de>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Wednesday, October 2, 2019 4:21:32 PM
Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster
labels
External Email - Use Caution
Hi Bronwyn,
thanks for the update and additional info.
I have to say that I have no very good clue at the moment.
Could you maybe upload an examplary file to the Freesurfer FileDrop at
https://gate.nmr.mgh.harvard.edu/filedrop2/ so that we can take a closer look?
Best regards,
Kersten
On Di, 2019-10-01 at 14:01 +1000, Bronwyn Overs wrote:
External Email - Use Caution
Hi Kersten,
Thank you for your detailed reply and sorry for this delayed response.
Yes the top row in my figure (attached again) was produced by using the
'--olab' argument with the 'mri_surfcluster' command and then loading each
cluster from a different label file. I attempted to follow your suggestion and
adjust the label 'threshold' in Freeview to minimum value in my significance
map (-5), but this did not display the missing regions - the surface remained
the same as row 1 of the attached figure.
To provide you with a little more detail about my method - am using
'mri_surfcluster' with the '--olab' argument to derive all of my significant
clusters of 100mm^2 or more. I am then using 'mri_label2label' to map each
label files (from the 'mri_surfcluster' command) back onto the images for each
of my individual subjects, and then generate subject level stats for each
cluster using 'mris_anatomical_stats'. At the moment I am concerned that the
subject level stats I have derived from my label files do not accurately
represent each significant cluster in totality as regions appear to be missing
even when i adjust the minimum threshold. As an alternative, when using
'mri_surfcluster', can I substitute the '--o', '--ocn', or '--oannot' arguments
for '--olab', and still perform my 'mri_label2label' and
'mris_anatomical_stats' steps?
Kind regards,
Bronwyn Overs
Research Assistant
[cid:1571816394.29396.7.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>
________________________________
From: "Kersten Diers, DZNE" <kersten.di...@dzne.de>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Sent: Thursday, September 5, 2019 2:13:50 AM
Subject: Re: [Freesurfer] Discrepancy between thresholded surface and cluster
labels
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:1571816394.29396.7.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>
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