I'm not sure those condition numbers include the pvr. Try loading the Xg.mat into matlab and computing
cond(Xg'*Xg)
Make sure Xg has the extra column for the pvr

On 12/3/2019 10:42 AM, Barletta, Valeria wrote:

Ok it worked.

So I tried with a non-zero vertex and I got:

Normalized matrix condition is 81.1382

Matrix condition is 30558.5

Found 149926 points in label.

Found 149926 voxels in mask

Saving mask to /autofs/space/lipari_001/users/valeria/NODDI/GLM//GLM_CME_ficvf_doug/rh_contrast-MS_CME_all_FIS_ICA1/mask.mgh

Reshaping mriglm->mask...

search space = 74490.928733

DOF = 18

Dumping voxel 1024 0 0 to /autofs/space/lipari_001/users/valeria/NODDI/GLM//GLM_CME_ficvf_doug/rh_contrast-MS_CME_all_FIS_ICA1/voxdump-1024-0-0

...and with a zero vertex and got:

Normalized matrix condition is 81.1382

Matrix condition is 30558.5

Found 149926 points in label.

Found 149926 voxels in mask

Saving mask to /autofs/space/lipari_001/users/valeria/NODDI/GLM//GLM_CME_ficvf_doug2/rh_contrast-MS_CME_all_FIS_ICA1/mask.mgh

Reshaping mriglm->mask...

search space = 74490.928733

DOF = 18

Dumping voxel 150252 0 0 to /autofs/space/lipari_001/users/valeria/NODDI/GLM//GLM_CME_ficvf_doug2/rh_contrast-MS_CME_all_FIS_ICA1/voxdump-150252-0-0

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Monday, December 2, 2019 2:56 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Question on GLM - correlation
oh, sorry, did not see the pvr. It could very well be the pvr that is causing the patchiness. Unfortunately, you have to debug it vertex by vertex. I would choose a few vertices (one with signal, on without) and run mri_glmfit with --voxdump vertexno 0 0 This will create a subfolder with the GLM for that vertex. I'm not sure what to tell you to look for, but I would at least check the condition numbers in each vertex. What is the nature of ficvf?

On 12/2/2019 1:22 PM, Barletta, Valeria wrote:
My other continuous variable is --pvr ${hemi}.ficvf.mgh

Not sure about --no-prune, I found it in my script as a default... Shall I remove it?

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Barletta, Valeria <VBARLETTA@mgh.harvard.edu>
Sent: Friday, November 29, 2019 3:08 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Question on GLM - correlation

Dear Freesurfers,

I am running glmfit to assess for correlation between y and another continue variable across the cortex (ficvf), correcting for the effect of age, using the command:

mri_glmfit \

--y {surfname_cme}.mgh \

--fsgd {contrast}.fsgd \

--C {contrast}.mat \

--pvr ${hemi}.ficvf.mgh" \

--surf fsaverage $hemi \

--glmdir ${glm_dir}/${hemi}_contrast-${contrast}_${surfname_cme} \

--no-prune

This is my matrix:

1 0 0

And my fsgd file:

Title CME

Class MS

Variable age

Input MS069_R01_01 MS 29

Input MS070_R01_02_R1year MS 44

Input MS072_R01_04 MS 38

Input MS073_R01_05 MS 47

Input MS075_R01_07_R1year MS 34

Input MS076_R01_08 MS 25

Input MS077_R01_09 MS 30

Input MS078_R01_10 MS 22

Input MS080_R01_12 MS 52

Input MS081_R01_13 MS 31

Input MS082_R01_14 MS 37

Input MS084_R01_16 MS 42

Input MS086_R01_18 MS 28

Input MS087_R01_19_R1year MS 39

Input MS088_R01_20 MS 44

Input MS089_R01_29 MS 44

Input MS090_R01_21 MS 32

Input MS091_R01_22 MS 32

Input MS092_R01_23 MS 36

Input MS094_R01_25 MS 47

Input MS104_R01_36 MS 52

This is the result:

Am I proceeding correctly?

Thank you,

Valeria
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