Re: [Freesurfer] Figures for publication

[Douglas N. Greve]

I would use either the ocn (cluster annotation) or the cluster-wise 
corrected map: overlay as you generally don't want to show uncorrected 
data. As for the max, it is a personal choice, just what you think looks 
good or makes your point.


On 4/22/2024 7:52 AM, Asuka Toyofuku wrote:


External Email - Use Caution

Dear Freesurfer experts,

Thanks to all the help from this community, we're finally done with 
GLM analysis(mri_glimfit) and the cluster-wise correction 
(mri_glmfit_sim), and now I'm making figures for publication.


My question is

1.
Which output mgh files are commonly used for making figures for
publication? Do people use, for example,
cache.th40.abs.sig.cluster.mgh (cluster-wise corrected map:
overlay) or cache.th40.abs.sig.masked.mgh (uncorrected sig values
masked by the clusters that survive correction) or even
uncorrected ones, such as sig.mgh file in the contrast directory
before running the correction? From my impression, not many people
use e.g., cache.th40.abs.sig.cluster.mgh (which shows no colour
gradation inside the clusters)...
2.
How do you select the colour-bar cut-off and max values? Most
publications I saw use min cut-off value: -log10(p) = 2.00 and
max: -log10(p) = 5.00, but some uses min: p=0.05 and max: p=0.01.
Obviously, if you set the max value (with the configure section)
very low (e.g., 2.0), the size of the cluster gets bigger and
looks more significant. Are there any suggestions for setting the
configure/threshold for the figures?


Many thanks,
Asuka



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[Freesurfer] Figures for publication

[Asuka Toyofuku]

External Email - Use Caution

Dear Freesurfer experts,

Thanks to all the help from this community, we're finally done with GLM 
analysis(mri_glimfit) and the cluster-wise correction (mri_glmfit_sim), and now 
I'm making figures for publication.

My question is

  1.
Which output mgh files are commonly used for making figures for publication? Do 
people use, for example, cache.th40.abs.sig.cluster.mgh (cluster-wise corrected 
map: overlay) or cache.th40.abs.sig.masked.mgh (uncorrected sig values masked 
by the clusters that survive correction) or even uncorrected ones, such as 
sig.mgh file in the contrast directory before running the correction? From my 
impression, not many people use e.g., cache.th40.abs.sig.cluster.mgh (which 
shows no colour gradation inside the clusters)...
  2.
How do you select the colour-bar cut-off and max values? Most publications I 
saw use min cut-off value: -log10(p) = 2.00 and max: -log10(p) = 5.00, but some 
uses min: p=0.05 and max: p=0.01. Obviously, if you set the max value (with the 
configure section) very low (e.g., 2.0), the size of the cluster gets bigger 
and looks more significant. Are there any suggestions for setting the 
configure/threshold for the figures?

Many thanks,
Asuka


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Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.