I send you also the maps corrected voxelwise, while the first images that I sent you were corrected clusterwise. Not sure this can help.
I tried to launch the command you suggested:
--voxdump 1024 0 0
but I got the error:
--voxdump: Command not found.
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
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.mghNot 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 - correlationDear 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 47Input MS104_R01_36 MS 52
This is the result:
Am I proceeding correctly?
Thank you,Valeria
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer