External Email - Use Caution
Thanks
If I have 4 groups
GroupDescriptorFile 1
Title XXX
Class G1
Class G2
Class G3
Class G4Input 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.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 >> >> >> > >-- >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 . 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
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