You need to include elements for the PVR regressors in your contrast. I see that you only have four elements in the examples below and four classes, so you will need to add more
On 6/9/2021 10:38 AM, stdp82@virgilio.it wrote:
External Email - Use Caution
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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18790.html https://secure-web.cisco.com/1zUXLBbd1KX4vgVXEwgoSHgSr-C0_UA1L6DQ_3GaGTQTrnW3FVVU-NaheSIMI8Ktb8w3d0gyQKPNCaquidO_nEa5BP-wa9ks42uSQ91iQsko8nq7RUOCMcr0a_BH2z2BrmVlxhfXOJkkl7wqWaF4iQBCwhcFe7J4Xp65eUy9vAVPOUsRc4EHJyIjD0rOz9xn6t2grnaYRAzjm4Tf_MFXquVVi4zbF0Ch3-NJE8wtUN_6FCPVNaYUy07FWLv-87qV_EW3p_5DlVp5NczslD09t3w/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg18790.htmlOn 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. StefanoGreat 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1eQw4HlVWpF4ZzzChk-hp9V02K-k7R250ksr-ZRpjXC5ESaaFuyzgAuTFAoGhyEgYrYKrou0EXi_1ri2KpbhLu0RDRiF8JbcjNXFPW9pDzwKVvda8OwJaDhfqmDKW60AffvShgjctqkjGDrtVh3d5g5ibXvHnKxBrCeDpGoDotLpWBCKfctMD7RKY5GYQlCh3Un1XOMnnDFI7_MF2lAwup2vGzl11XZ_ZrOq3M8ZZB588KJPu216UQ-0rXaUfyN9kqO2LvtMM_BKWPkbPWLv1wQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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 Partners Compliance HelpLine at *MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be* http://www.partners.org/complianceline http://secure-web.cisco.com/1SUkt2fsByhbVkrjyleWea7U8vPw7dJUUjO3n73A05t_91lBe900zX8Xj5BXS5FVVIPhPdXp82Z6tn-yeqKFAhUFk_5StCCsEPSU9TJVMOayzf4j0KrCyoFNj-C2OGDP0xFemZL4QAwmVXf6LLrOE9uXSoUkhZAdqVKfMGyQ69ZkTVjm5-iFg90fsEAVNWEfQKIfNgsAMcDyfxfoi3sAh7AkPp30_dgubiPt_de-c2xl98NuTVZv4kCbN3juzQ9BiEeSE28aMxZczxiclrU7Fxg/http%3A%2F%2Fwww.partners.org%2Fcomplianceline . If the e-mail was sent to you in
error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://secure-web.cisco.com/1eQw4HlVWpF4ZzzChk-hp9V02K-k7R250ksr-ZRpjXC5ESaaFuyzgAuTFAoGhyEgYrYKrou0EXi_1ri2KpbhLu0RDRiF8JbcjNXFPW9pDzwKVvda8OwJaDhfqmDKW60AffvShgjctqkjGDrtVh3d5g5ibXvHnKxBrCeDpGoDotLpWBCKfctMD7RKY5GYQlCh3Un1XOMnnDFI7_MF2lAwup2vGzl11XZ_ZrOq3M8ZZB588KJPu216UQ-0rXaUfyN9kqO2LvtMM_BKWPkbPWLv1wQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer