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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu Sent: Monday, December 2, 2019 2:56 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Barletta, Valeria VBARLETTA@mgh.harvard.edumailto:VBARLETTA@mgh.harvard.edu Sent: Friday, November 29, 2019 3:08 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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: [cid:part5.EF2B16D0.6F355EBE@mgh.harvard.edu][cid:part6.DCB6E7A8.EAB1A47E@mgh.harvard.edu]
Am I proceeding correctly?
Thank you, Valeria
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