mri_glmfit with pvr - Freesurfer

9 Jun 2021


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Thanks
If I have 4 groups
GroupDescriptorFile 1
Title XXX
Class G1
Class G2
Class G3
Class G4
Input subj1 G1
Input subj2 G3
Input subj3 G2
Input subj4 G2
Input subj5 G4
....
Are the contrasts below corrected?
G1_only_thick 1 0 0 0
G2_only_thick 1 0 0 0
G3_only_thick 1 0 0 0
G4_only_thick 1 0 0 0
G1+G2-G3+G4_thick 0.5 0.5 -0.5 -0.5
G3+G4+G2+G1_thick -0.5 -0.5 0.5 0.5
G1+G2+G3+G4_thick 0.25 0.25 0.25 0.25
Thanks
Stefano
Yes, you use a "per-vertex map" (--pvr option to mri_glmfit). See, example, this thread https://secure-web.cisco.com/1AQW2Zmfaui0gjHDqfC-62qKrikS49RYbR7pNeQeTr2onen... 6/3/2021 10:22 AM, std...@virgilio.it wrote:
...
External Email - Use Caution Hi, how can I perform vertex by vertex (surface) analysis of covariance between functional connectivity data (FS-FAST) and cortical thickness, regressing out the effect of groups?My mean concern is how buid the fsgd file. Stefano
Great news, thank you, Doug! Best, aga On 8/3/11 5:02 PM, "Douglas N Greve" gr...@nmr.mgh.harvard.edu wrote:
...
Hi Aga, what you have done is correct, no need to include the pvr in the
fsgd.
doug
Burzynska, Aga wrote:
...
Dear all,
I am trying to make group level analysis of functional data on the
surface and add per-vertex regressors (PVR, here: cortical thickness)
into the design. When I view the results I have the feeling that the PVR
is not really included in the model:
I am using the command:
mri_glmfit --glmdir lh_output --y cope1_lh_4D.mgh --fsgd
Group1versusGroup2.fsgd  --pvr lh.thickness.10.mgh --C
Group1only_thickness.mat --C Group2only_thickness.mat --C
Group1minusGroup2_thickness.mat --C Group2minusGroup1_thickness.mat --C
Group1plusGroup2_thickness.mat
where
cope1_lh_4D.mgh contains the concatenated sig.mgh images from the fixed
level analysis (combining the runs) for each participant
fsgd file contains:
GroupDescriptorFile 1
Title Group1versusGroup2
Class Group1 
Class Group2
Input     1109     Group1
Input     1110     Group1
Input     1111     Group1
Input     1112     Group1
...
Input     2280      Group2
Input     2282  Group2
Input     2283  Group2
Input     2284  Group2
The PVR is a file containing thickness maps for each participant,
concatenated in the same order as for the functional data.
So there are 2 main regressors (1 factor, 2 levels), but the contrast
files contain 3 regressors (the third one is the PVE), for instance:
Group1minusGroup2_thickness.mat contains  1 -1 0.
Does it look correct?
Should the pvr regressor be included in the fsdg file? How can I do it?
Thank you very much for your help,
Cheers,
Aga

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