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:8310494e-35a4-4aba-b586-ab908982ab21][cid:a9e74150-3e3a-4e1c-ac08-07bfe4e40dba]
Am I proceeding correctly?
Thank you, Valeria
I'm not sure what you are doing here. You say that you have two continuous variables, but there is only one in the fsgd file. The contrast has 3 items, but it would test for the offset, not the slope. Also, why do you have --no-prune?
On 11/29/2019 3:08 PM, Barletta, Valeria wrote: 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:part1.9EE9F34D.23B9DFF4@mgh.harvard.edu][cid:part2.A1889CBE.3AAE2CA4@mgh.harvard.edu]
Am I proceeding correctly?
Thank you, Valeria
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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: [cid:8310494e-35a4-4aba-b586-ab908982ab21][cid:a9e74150-3e3a-4e1c-ac08-07bfe4e40dba]
Am I proceeding correctly?
Thank you, Valeria
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:part1.1172E934.FDC7214E@mgh.harvard.edu][cid:part2.77706C41.78922B9E@mgh.harvard.edu]
Am I proceeding correctly?
Thank you, Valeria
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freesurfer@nmr.mgh.harvard.edu
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Barletta, Valeria -
Greve, Douglas N.,Ph.D.