I did what you suggested in your previous email:
> That does not have the pvr in it. You can extract the pvr for that
> vertex and add it as a column to the X matrix with
> pvr = fast_vol2mat(MRIread('pvr.mgz'));
> pvrvtx = pvr(:,vertexno+1);
Which file shall I look like for the single voxel?
________________________________
From: Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu>
Sent: Thursday, December 5, 2019 12:40 PM
To: Barletta, Valeria <vbarle...@mgh.harvard.edu>; Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Question on GLM - correlation
On 12/4/19 11:51 AM, Barletta, Valeria wrote:
> Ok I did it and did not get any .mgh file as a result.
Did what?
>
> At this point I wonder, what is the best model to check for
> correlation between my continuous outcome CME.mgh and the continuous
> variable ficvf.mgh?
> Shall I include ficvf.mgh as a regressor (pvr) and use the Contrast 1
> 0 0 or shall I use a completely different method?
>
> Thanks, sorry for the long interaction...
> ------------------------------------------------------------------------
> *From:* Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu>
> *Sent:* Tuesday, December 3, 2019 3:18 PM
> *To:* Barletta, Valeria <vbarle...@mgh.harvard.edu>; Freesurfer
> support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] Question on GLM - correlation
> That does not have the pvr in it. You can extract the pvr for that
> vertex and add it as a column to the X matrix with
> pvr = fast_vol2mat(MRIread('pvr.mgz'));
> pvrvtx = pvr(:,vertexno+1);
>
> ps. Please remember to post to the list
>
> On 12/3/2019 1:29 PM, Barletta, Valeria wrote:
>> Ok done. This is the Xg.mat
>> 1 29
>> 1 44
>> 1 38
>> 1 47
>> 1 34
>> 1 25
>> 1 30
>> 1 22
>> 1 52
>> 1 31
>> 1 37
>> 1 42
>> 1 28
>> 1 39
>> 1 44
>> 1 44
>> 1 32
>> 1 32
>> 1 36
>> 1 47
>> 1 52
>> And the cond(Xg'*Xg) is again: 3.0555e+04
>> Looks like there is no extra column for the pvr in the Xg.mat
>>
>>
>> ------------------------------------------------------------------------
>> *From:* Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu>
>> <mailto:dgr...@mgh.harvard.edu>
>> *Sent:* Tuesday, December 3, 2019 11:03 AM
>> *To:* Barletta, Valeria <vbarle...@mgh.harvard.edu>
>> <mailto:vbarle...@mgh.harvard.edu>; Freesurfer support list
>> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu>
>> *Subject:* Re: [Freesurfer] Question on GLM - correlation
>> 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-boun...@nmr.mgh.harvard.edu
>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>>> <freesurfer-boun...@nmr.mgh.harvard.edu>
>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve,
>>> Douglas N.,Ph.D. <dgr...@mgh.harvard.edu>
>>> <mailto:dgr...@mgh.harvard.edu>
>>> *Sent:* Monday, December 2, 2019 2:56 PM
>>> *To:* freesurfer@nmr.mgh.harvard.edu
>>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>>> <freesurfer@nmr.mgh.harvard.edu> <mailto: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-boun...@nmr.mgh.harvard.edu
>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>>>> <freesurfer-boun...@nmr.mgh.harvard.edu>
>>>> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
>>>> Barletta, Valeria <vbarle...@mgh.harvard.edu>
>>>> <mailto:vbarle...@mgh.harvard.edu>
>>>> *Sent:* Friday, November 29, 2019 3:08 PM
>>>> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
>>>> <mailto: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
>>>>
>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>
>
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