This is actually a very obscure feature of freesurfer that takes some
explaining. In FS, all p-values are computed with a two-sided test (so
the sig.mgh represents a signed p-value). When you pass --sign pos to
mri_surfcluster, it sees that you want to do a signed test instead of an
unsigned test, so it essentially changes the sig.mgh internally to
create unsigned p-values. Signed is more powerful than unsigned so you
can get more clusters than the equivalent unsigned test. But when you
look at the sig.mgh in freeview, you are looking at unsigned p-values.
You could change the sig.mgh to signed p-values and then it should match
what you are seeing in the summary file. Or you can simply change the
threshold in freeview from 2 (= -log10(.01)) to 1.7 (= -log10(.02)).
Sorry, I know this is confusing...
On 2/22/2023 8:59 PM, Smith, Christine wrote:
External Email - Use Caution
Hi Yujing,
Thank you for explaining that.
I believe that mri_surfcluster is the correct output, in that it is
carrying out a one-sided test of significance at 2 (Sig =
-log(pvalue), i.e., p < 0.01).
For the Configure options, is there a similar option to allow the
threshold to be 2 for a one-sided test?
We have experimented around by setting very high (max) and very low
(min) values and we still weren't able to get the clusters identified
by mri_surfclust to show up on Freeview, even when we reduce the
threshold to account for the fact that it is a two-sided test.
Christine
--
Christine N. Smith, Ph.D.
Research Service, VA San Diego Healthcare System
Department of Psychiatry, University of California San Diego
VA San Diego Healthcare System
VMRF Building 13
3350 La Jolla Village Drive (151A)
San Diego, CA 92161
T: (858) 552-8585; then press *7128
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Huang, Yujing
<yhuan...@mgh.harvard.edu>
*Sent:* Wednesday, February 22, 2023 1:02 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] different clusters in mri_surfcluster
output versus viewing in Freeview
Hi Christine,
Sig = -log(pvalue)
In freeview, the overlay thresholds can be adjusted by clicking
‘Configure’ button (under the Overlay dropdown menu).
For mri_surfcluster (*MailScanner has detected a possible fraud
attempt from "secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_surfcluster),
<https://secure-web.cisco.com/12Z5LTWKJFy49SY9EYkSRL39OTupsZodDE6ECdqjWfTtWVRzmYfIFTjDnIU5M8GwCXg9p90FqCJjbaMfQ8u7SMJ38lufZp5OCKjfcfwggzOVGIzhL1B165gWXJ96OdxMJmnOMHqV93K2mkyLP5Yh7X1F3wX3wDV92D8JPdG80cuENmN8zrL6eWbPbR0XZ1jmBtGXTQ1yXsX5T8fNspjiVREhM-BJaaxp6XOPVHKpmaMDic0YAjwARlg5o0lWNCGuqa0Drz1uJYRHBS7lDpvXoduFeHq5t_JysVrJ7D0Gab_lo-_YG3EBe75OoE0WyOCNaol3cMJrNyd8GvkrtDCRjyg/https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_surfcluster%29%2C__%3B%21%21LLK065n_VXAQ%21nP6YzWkD5kki_fH6eoPxh7GYGISZOCVDkiv7oh7i7miyEbAYhc-kerXLBeVJsEdOL47Z-BwyKRfHb1Azt_RymKoiIqg%24>
I think you can try to adjust these options to match freeview: --thmin
<>, --thmax <>, --thsign <>, --minarea <>, --no-adjust.
Best,
Yujing
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Smith, Christine
*Sent:* Tuesday, February 21, 2023 6:01 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] different clusters in mri_surfcluster output
versus viewing in Freeview
* External Email - Use Caution *
Hello,
I am getting a mismatch of clusters when we view cluster results in
freeview versus ask for a table of the significant clusters.
I am performing a GLM analysis on Freesurfer to analyze cortical
thickness (mri_glmfit). When viewing the significance map with
freeview, we set the minimum threshold to 2 for the sig.mgh file.
We also used the same threshold when creating a summary table of the
clusters using mri_surfcluster.
mri_surfcluster --in {$dir}/visuospatial_MCI_correlation/sig.mgh
--hemi left --thmin 2 --thsign pos --minarea 10 --subject fsaverage
--surf inflated --annot BN_Atlas --sum
{$dir}/visuospatial_MCI_correlation/left.thickness.clustersummary_BN.txt
We were hoping to use the summary text file to identify the clusters
on freeview and their characteristics (e.g., size, x, y, z
ccordinates). Unfortunately, the regions that we see for both methods
don’t match as there are some clusters that we see on the summary text
file that we don’t see on freeview and vice versa. How can we make the
output of these two methods match up? Note that the issue is not the
minimum cluster size in the summary table. When we put that to 1 we
still get a mismatch.
Please note that in the mri_surfcluster program we can indicate that
we only want positive results. We don't see a way to do this in
freeview or a way for that to affect the p value in freeview.
Is this possibly the issue? If so, how can we make a picture in
freeview that matches our summary table?
Regards,
Christine
--
Christine N. Smith, Ph.D.
Research Service, VA San Diego Healthcare System
Department of Psychiatry, University of California San Diego
VA San Diego Healthcare System
VMRF Building 13
3350 La Jolla Village Drive (151A)
San Diego, CA 92161
T: (858) 552-8585; then press *7128
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