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Thanks a lot. Sorry if I bother you again: If I want to remove thickness, age and gender as nuisance variables; My FSGD file should be:

GroupDescriptorFile 1 Title Func Class HC Class CMT Variables Age gender Input fs_VF HC 46 Female Input fs_RF HC 24 Female .......

My group.diff.mtx should be: 1 -1 0 0 0 0 0

Is it ok?

Thanks a lot Raffaele

Il giorno gio 3 gen 2019 alle ore 20:11 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:

The contrast is not correct for your design. Your design matrix will have 3 columns, one for HC, one for CMT, and one for rh.thickness_30.fsavg.mgh. Ie, it automatcailly interprets PVRs in a DOSS kind of way. If you want to test for a difference in thickness-meylin slopes between the two groups, you will need to have two PVRs, one where the value is the thickness for HC subjects and 0 for CMT subjects, the other the reverse, then set your contrast to 0 0 1 -1. If you just want to remove thickness as a nuisance, then you can stick with what you have and just use a contrast of 1 -1 0

On 12/25/18 5:05 AM, Raffaele Dubbioso wrote:

...

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Dear Freesurfer team,

I'm running a group analysis where I'd like to compare myelination between two groups regressing out cortical thickness. Unfortunately I get always the same error message: dimension mismatch between X and contrast group.diff.mtx X has 3 cols, C has 4 cols. Is my group.mtx correct?

My command line is: mri_glmfit --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd thickness.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --C group-x-thick --Cg1g2.intercept.mts --C g1g2.thick.mtx --surf fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness.glmdir

My group_diff.mtx: 1 -1 0 0

This is my FSGD FILE: GroupDescriptorFile 1 Title Myelin Class HC Class CMT Inputfs_VFHC ........

Thank you very much for your help

Best regards, Raffaele

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Thanks, but I got the following error message:

RROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd age_gender.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --surf fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness_age_gender.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.000000 (col 5), Max=146.140350 (col 3) The scale is much different between columns 5 and 3, you may want to normalize by subtracting the mean and dividing by the standard deviation. Column 5, all values are 0 Column 6, all values are 0 Columns 5 and 6 are the same

Il giorno dom 6 gen 2019 alle ore 20:18 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:

yes, that is the right contrast

On 1/5/19 7:30 AM, Raffaele Dubbioso wrote:

    External Email - Use Caution

Thanks a lot. Sorry if I bother you again: If I want to remove thickness, age and gender as nuisance variables; My FSGD file should be:

GroupDescriptorFile 1 Title Func Class HC Class CMT Variables Age gender Input fs_VF HC 46 Female Input fs_RF HC 24 Female .......

My group.diff.mtx should be: 1 -1 0 0 0 0 0

Is it ok?

Thanks a lot Raffaele

Il giorno gio 3 gen 2019 alle ore 20:11 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:

...

The contrast is not correct for your design. Your design matrix will have 3 columns, one for HC, one for CMT, and one for rh.thickness_30.fsavg.mgh. Ie, it automatcailly interprets PVRs in a DOSS kind of way. If you want to test for a difference in thickness-meylin slopes between the two groups, you will need to have two PVRs, one where the value is the thickness for HC subjects and 0 for CMT subjects, the other the reverse, then set your contrast to 0 0 1 -1. If you just want to remove thickness as a nuisance, then you can stick with what you have and just use a contrast of 1 -1 0

On 12/25/18 5:05 AM, Raffaele Dubbioso wrote:

...

    External Email - Use Caution

Dear Freesurfer team,

I'm running a group analysis where I'd like to compare myelination between two groups regressing out cortical thickness. Unfortunately I get always the same error message: dimension mismatch between X and contrast group.diff.mtx X has 3 cols, C has 4 cols. Is my group.mtx correct?

My command line is: mri_glmfit --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd thickness.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --C group-x-thick --Cg1g2.intercept.mts --C g1g2.thick.mtx --surf fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness.glmdir

My group_diff.mtx: 1 -1 0 0

This is my FSGD FILE: GroupDescriptorFile 1 Title Myelin Class HC Class CMT Inputfs_VFHC ........

Thank you very much for your help

Best regards, Raffaele

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Raffaele Dubbioso, MD, PhD University Federico II of Naples Department of Neurosciences, Reproductive Sciences and Odontostomatology. Via Sergio Pansini, 5 80131 Napoli, ITALY phone: +39-0817464579 fax: +39-0817462667

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