It looks like you are doing the right thing. You indicated not to use a contrast matrix. If you want to test a contrast, I think the matrix would be [0 1] (I think it adds an offset regressor)

On 2/10/2023 4:50 PM, Finn, Quentin wrote:

        External Email - Use Caution        

Freesurfer experts,

I have some surface data that I'd like to correlate with some other data, although a linear regression would also be fine if I could get something like a t-stat out of it. 

This data came from two different PET tracers -- voxelwise data was resampled via vol2surf onto each subjects cortical surface:

So I have, say, data like this:

tracer1_subj1_lh.mgh
tracer1_subj2_lh.mgh
.
.
.
.
tracer1_subjn_lh.mgh

And then I have another set:

tracer2_subj1_lh.mgh
tracer2_subj2_lh.mgh
.
.
.
.
tracer2_subjn_lh.mgh

I'd really like to just stack them all up with mris_preproc, something like this:

mris_preproc --is tracer1_subj1_lh.mgh --is tracer1_subj2_lh.mgh [etc] --is tracer1_subjn_lh.mgh --out tracer1_lh.mgh --hemi lh --fsgd tracer1.fsgd
mris_preproc --is tracer2_subj1_lh.mgh --is tracer2_subj2_lh.mgh [etc] --is tracer2_subjn_lh.mgh --out tracer2_lh.mgh --hemi lh --fsgd tracer1.fsgd

The FSGD's are the same because the subjects are the same.


and then run something like...

mri_glmfit  --glmdir tracer1_tracer2_left --y tracer1_lh.mgh --fsgd tracer1.fsgd --pvr tracer2.mgh --no-contrasts-ok --surface fsaverage lh

This doesn't have an output that's really what I'm looking for as far as I can tell though, there's no fit statistics type overlay in the output folder, probably because I'm doing something wrong.

Any help on this would be just wonderful!

-quentin finn


Houston Methodist. Leading Medicine.

U.S. News & World Report has named Houston Methodist Hospital the Best Hospital in Texas for 11 years in a row. Houston Methodist is the No. 1 hospital in Texas and No. 15 in the nation. For more than 100 years, Houston Methodist has provided the best — and safest — clinical care, advanced technology and patient experience. That is our promise of leading medicine.


MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be houstonmethodist.org
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be twitter.com/MethodistHosp
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be facebook.com/HoustonMethodist

***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer