External Email - Use Caution
Ah I see. Great, thanks Doug!!
Best,
Panos
From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas N. Greve"
<dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Tuesday, August 11, 2020 at 10:37 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [External] Re: Comparing surface maps
If you want to compare the maps, then the contrast would be [0 1]
Imagine a scatter plot at each vertex with the values for one map on the x axis
and the values for the other map on the y
You then fit a straight line (offset and slope). The sig test will be for
0*offset+1*slope = slope
If you add a covariate, then the contrast would be [0 0 1]
On 8/11/2020 3:13 AM, Fotiadis, Panagiotis wrote:
External Email - Use Caution
Hi Doug,
That’s extremely helpful, thank you! And just to verify:
1. Since I have 1 group and I just want to compare the two surface maps
(without adjusting for other covariates like age/sex at the moment), my
contrast matrix should be [1 0], right?
2. If I add other covariates (let’s say age for instance), then if I want to
test the hypothesis that the two regional maps are sig. different from each
other after regressing the effects of age, would my contrast matrix then be [1
0 0]?
Best,
Panos
From:
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of "Douglas N. Greve"
<dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
Reply-To: Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Date: Monday, August 10, 2020 at 9:57 AM
To: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: [External] Re: [Freesurfer] Comparing surface maps
Try this
To regress include a per-vertex regressor (PVR, --pvr) in mri_glmfit.
This procedure will essentially add a column to the design matrix for
each vertex. Eg, if your FSGD file (my.fsgd) has two groups, then, by
itself, the design matrix would be two columns, one for each group.
You will pass mri_glmfit two maps (one with --y, the input), and one
the PVR; each map will have a frame for each subject. For a given
vertex, the PVR values for each subject will be extracted and added as
a column to the design matrix; the design matrix will be fit to the
y-values for that vertex, the contrast matrices will be applied, and
p-values computed. The extra column in the design matrix needs to be
accounted for in the contrast matrix. Eg, if you have two groups, then
you might have a contrast of +1 -1. If you are going to treat the PVR
as a nuisance variable, then you would add a 0 (so +1 -1 0). If the
PVR is a regressor of interest, then you could use 0 0 +1. Multiple
PVRs can be added to make more complicated designs and test more
complicated PVR hypotheses. DOSS and DODS do not apply to PVR. All the
same rules about design matrices do apply (eg, scaling and
colinearity). Permutation does not work with PVR.
Eg, create two maps, thickness and curvature, with
mris_preproc --f my.fsgd --hemi lh --meas thickness --o thickness.lh.sm00.mgz
mris_preproc --f my.fsgd --hemi lh --meas curv --o curv.lh.sm00.mgz
When you create your contrast matrices, make sure to include an item
for the PVR.
mri_glmfit --y thickness.lh.sm00.mgz --fsgd my.fsgd --C contrast.mtx
--pvr curv.lh.sm00.mgz --o my.glm --surf fsaverage lh
On 8/10/2020 1:29 AM, Fotiadis, Panagiotis wrote:
External Email - Use Caution
Hello FS experts,
I have a cohort of subjects for whom I created cortical thickness and T1w/T2w
signal ratio surface maps, projected them to fsaverage’s surface, smoothed
them, and then created average thickness and T1w/T2w maps using mris_preproc.
Is there a way to statistically compare the two averaged surface maps (i.e.,
come up with a third surface map displaying correlation patterns between
thickness and T1w/T2w signal across the surface)?
Thanks in advance!
Best,
Panos
_______________________________________________
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<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
