This is the kind of thing that happens with clusterwise corrections. It
is hard to predict what happens. When you raise the threshold, you lose
some of the activation in your real map (ie, clusters become smaller).
But in the Null map, clusters also become smaller. So, at the lower
threshold, the frequency of a cluster of a size in your real data may be
high (so you have a high clusterwise p-value). When you raise the
threshold, the real data has a new (smaller) cluster size, but in the
Null map, the frequency of that clustersize may be low (and so a lower
(ie, more sig) clusterwise p-value). It's confusing, I know.
On 9/29/2023 3:35 PM, Guthrie, Andrew J. wrote:
External Email - Use Caution
Hi all,
I took the freesurfer course in the recent past, and I am now
beginning to run some glm thickness analyses!
Currently I am doing a thickness analysis looking at the difference
between two groups while controlling for age, and two continuous
measures of depression and anxiety. The general commands I run are as
follows:
mris_preproc --fsgd [fsgd filename] --cache-in
thickness.fwhm10.fsaverage --target fsaverage --hemi lh --o
lh.[filename].thickness.10.mgh
mris_preproc --fsgd [fsgd filename] --cache-in
thickness.fwhm10.fsaverage --target fsaverage --hemi rh --o
rh.[filename].thickness.10.mgh
mri_glmfit --y lh.[filename].thickness.10.mgh --fsgd [fsgd filename]
doss --C contrast.mtx --surf fsaverage lh --glmdir
lh_[filename]_fwhm10.glmdir
mri_glmfit --y rh.[filename].thickness.10.mgh --fsgd [fsgd filename]
doss --C contrast.mtx --surf fsaverage rh --glmdir
rh_[filename]_fwhm10.glmdir
mri_glmfit-sim --glmdir lh_[filename]_fwhm10.glmdir --cwpvalthresh .05
--cache 2.0 abs --2spaces
mri_glmfit-sim --glmdir rh_[filename]_fwhm10.glmdir --cwpvalthresh .05
--cache 2.0 abs --2spaces
I noticed that in some analyses there would be no significant clusters
when the threshold is set at 2.0 (p<0.01) but if you were to run the
same analyses with a threshold at 2.3 (p<0.005) there would be a
significant cluster, in the lingual for example. If I go one step
further and set the threshold to 3.0 there is also a significant
cluster – however the cluster is now in the isthmuscingulate.
Am I doing something incorrectly or is this possible? And if so, could
you help me understand what is going on here.
Best,
Andrew
_______________________________________________
Freesurfer mailing list
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
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
<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.
