Re: [Freesurfer] mri_glmfit error: matrix is rank-deficient by 18

[Shawn Flanagan]

External Email - Use Caution

Hi,

This doesn't make a difference. I can say that the Apple M- dev version
likely has an issue with the permutation procedure in runClustSims.sh. At
the GLM stage, the program is still saying that the matrix is rank
deficient by the number of matrix entries (18).

Best,
Shawn

On Sat, Oct 5, 2024 at 9:38 PM fsbuild  wrote:

>
> I’m not sure it will make a difference, but you could try downloading,
> installing and running one of the current development builds for the
> Silicon Mac.  You could try this download link,
>
> https://surfer..
> nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/stable/freesurfer-macOS-darwin_arm64-dev.pkg
>
>
> - R.
>
> On Oct 4, 2024, at 12:20, Shawn Flanagan <
> shawn.flana...@rosalindfranklin.edu> wrote:
>
> External Email - Use Caution
>
> *Hi FreeSurfer Developers,*
>
> *I am attempting to compute group analysis as described in the FS tutorial
> and it appears to run but with the following message at the end for each
> contrast:*
>
> Writing results
>   CON-ACLleft
> maxvox sig=-2.57471  F=9.30914  at  index 155198 0 0seed=1728409464
> Computing efficiency
> /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
> vnl_qr::solve() : matrix is rank-deficient by 18
> /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
> vnl_qr::solve() : matrix is rank-deficient by 18
> /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
> vnl_qr::solve() : matrix is rank-deficient by 18
> /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
> vnl_qr::solve() : matrix is rank-deficient by 18
> /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
> vnl_qr::solve() : matrix is rank-deficient by 18
> /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
> vnl_qr::solve() : matrix is rank-deficient by 18
> /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
> vnl_qr::solve() : matrix is rank-deficient by 18
> /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
> vnl_qr::solve() : matrix is rank-deficient by 18
> /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
> vnl_qr::solve() : matrix is rank-deficient by 18
> /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
> vnl_qr::solve() : matrix is rank-deficient by 18
> /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
> vnl_qr::solve() : matrix is rank-deficient by 18
> /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
> vnl_qr::solve() : matrix is rank-deficient by 18
> /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13..2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
> vnl_qr::solve() : matrix is rank-deficient by 18
> /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
> vnl_qr::solve() : matrix is rank-deficient by 18
> /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
> vnl_qr::solve() : matrix is rank-deficient by 18
> /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
> vnl_qr::solve() : matrix is rank-deficient by 18
> /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
> vnl_qr::solve() : matrix is rank-deficient by 18
> /Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
> vnl_qr::solve() : matrix is rank-deficient by 18
>   CON-ACLright
> maxvox sig=2..

Re: [Freesurfer] mri_glmfit error: matrix is rank-deficient by 18

[fsbuild]

External Email - Use Caution

 I’m not sure it will make a difference, but you could try downloading, 
installing and running one of the current development builds for the Silicon 
Mac.  You could try this download link,
https://secure-web.cisco.com/1knximumtc7HGhko0zDsKDfS2Nqhp3y3blHXGS-mPKcRQ-2luavC6Mq9rvDUJYmUM_VbyhxAAIBhGwI31zlmxUtqwDUNwa4YthPxUvazsca50xAOHgKTqwZiT6-xSv-TigJXP41F06y1wQ2hv5FQINurFhlYJSd3kvnYeiKf3yr-H9mJQgLpuJeTgYsb9w5GRt9VWSpFSYvgj38dbu76zQiUysDyRGMKr9EJ8QN6S2z9adVQ21A7L5-tsy90yaWA3WUmhVR180cvBo6m3TNg0LZFnYHWbh2Fd1YzjuBjEpgQqGOWnytWPYTIbzKjhngHS/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev%2Fstable%2Ffreesurfer-macOS-darwin_arm64-dev.pkg
- R.

On Oct 4, 2024, at 12:20, Shawn Flanagan 
 
wrote:External Email - Use 
CautionHi FreeSurfer Developers,
I am attempting to compute group analysis as described in the FS tutorial and 
it appears to run but with the following message at the end for each 
contrast:
Writing results
  CON-ACLleft
    maxvox sig=-2.57471  F=9.30914  at  index 155198 0 
0    seed=1728409464
Computing efficiency
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4..13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13..2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
 vnl_qr::solve() : matrix is rank-deficient by 18
  CON-ACLright
    maxvox sig=2.75772

[Freesurfer] mri_glmfit error: matrix is rank-deficient by 18

[Shawn Flanagan]

External Email - Use Caution

*Hi FreeSurfer Developers,*

*I am attempting to compute group analysis as described in the FS tutorial
and it appears to run but with the following message at the end for each
contrast:*

Writing results
  CON-ACLleft
maxvox sig=-2.57471  F=9.30914  at  index 155198 0 0seed=1728409464
Computing efficiency
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
  CON-ACLright
maxvox sig=2.75772  F=10.1304  at  index 31842 0 0seed=1728409464
Computing efficiency
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matrix is rank-deficient by 18
/Users/developer/space_freesurfer/build/tulum/trunk/developer-dev/packages/4.13.2/itk/4.13.2/src/ITK/Modules/ThirdParty/VNL/src/vxl/core/vnl/algo/vnl_qr.hxx:
vnl_qr::solve() : matr

Re: [Freesurfer] mri_glmfit-sim - Clusterwise correction for multiple comparisons.

[Douglas N. Greve]

This is the kind of thing that happens with clusterwise corrections. It 
is hard to predict what happens. When you raise the threshold, you lose 
some of the activation in your real map (ie, clusters become smaller). 
But in the Null map, clusters also become smaller. So, at the lower 
threshold, the frequency of a cluster of a size in your real data may be 
high (so you have a high clusterwise p-value). When you raise the 
threshold, the real data has a new (smaller) cluster size, but in the 
Null map, the frequency of that clustersize may be low (and so a lower 
(ie, more sig) clusterwise p-value). It's confusing, I know.


On 9/29/2023 3:35 PM, Guthrie, Andrew J. wrote:


External Email - Use Caution

Hi all,

I took the freesurfer course in the recent past, and I am now 
beginning to run some glm thickness analyses!


Currently I am doing a thickness analysis looking at the difference 
between two groups while controlling for age, and two continuous 
measures of depression and anxiety. The general commands I run are as 
follows:


mris_preproc --fsgd [fsgd filename] --cache-in 
thickness.fwhm10.fsaverage --target fsaverage --hemi lh --o 
lh.[filename].thickness.10.mgh


mris_preproc --fsgd [fsgd filename] --cache-in 
thickness.fwhm10.fsaverage --target fsaverage --hemi rh --o 
rh.[filename].thickness.10.mgh


mri_glmfit --y lh.[filename].thickness.10.mgh --fsgd [fsgd filename] 
doss --C contrast.mtx --surf fsaverage lh --glmdir 
lh_[filename]_fwhm10.glmdir


mri_glmfit --y rh.[filename].thickness.10.mgh --fsgd [fsgd filename] 
doss --C contrast.mtx --surf fsaverage rh --glmdir 
rh_[filename]_fwhm10.glmdir


mri_glmfit-sim --glmdir lh_[filename]_fwhm10.glmdir --cwpvalthresh .05 
--cache 2.0 abs --2spaces


mri_glmfit-sim --glmdir rh_[filename]_fwhm10.glmdir --cwpvalthresh .05 
--cache 2.0 abs --2spaces


I noticed that in some analyses there would be no significant clusters 
when the threshold is set at 2.0 (p<0.01) but if you were to run the 
same analyses with a threshold at 2.3 (p<0.005) there would be a 
significant cluster, in the lingual for example. If I go one step 
further and set the threshold to 3.0 there is also a significant 
cluster – however the cluster is now in the isthmuscingulate.


Am I doing something incorrectly or is this possible? And if so, could 
you help me understand what is going on here.


Best,

Andrew


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Re: [Freesurfer] mri_glmfit-sim - Clusterwise correction for multiple comparisons.

[John Anderson]

External Email - Use Caution

assuming that all preprocessing steps, fsgd file and contrasts are correct,
the choice between doss and dods could explain some of the variability
you're seeing in your results. Consider running both models and possibly
additional validation to see which model better fits your data. Each model
assumes a different relationship between your groups and covariates, and
they can yield different results because of these assumptions.
DOSS: In this model, the assumption is that all groups are affected by the
covariates in the same way, i.e., they have the same slope but may have
different intercepts. Essentially, it assumes that the effect of your
covariates (age, depression, anxiety) is constant across all groups. Any
variability among groups will be captured in the intercept term.
DODS: This model allows each group to have a different relationship with
the covariates. It assumes that both the slopes and the intercepts can
differ across groups. In this case, not only can the groups differ in terms
of their mean values (offset), but they can also differ in how they relate
to the covariates (slope).
If you use DOSS but the truth is more akin to DODS, you might underestimate
the variability in the relationships between groups and covariates, which
could potentially lead to the kinds of inconsistencies you've observed.
Conversely, choosing DODS when DOSS would be sufficient could introduce
unnecessary complexity and consume degrees of freedom, which might affect
the statistical power.
Given your focus on nuances like controlling for age, depression, and
anxiety, it would be worth scrutinizing how these covariates interact with
your groups. If you suspect different groups could indeed have a different
relationship with these covariates, DODS might be more appropriate.
Finally, The results you are observing appear to be false positives, likely
due to the use of a lenient statistical significance threshold in your
surface-based analysis. Opting for a more rigorous threshold, such as a
cache=4, is generally a solid choice, particularly when you don't have a
specific hypothesis about the location of significance of correlation and
are conducting exploratory analyses

On Fri, Sep 29, 2023 at 3:38 PM Guthrie, Andrew J. <
ajguth...@mgh.harvard.edu> wrote:

> External Email - Use Caution
>
> Hi all,
>
>
>
> I took the freesurfer course in the recent past, and I am now beginning to
> run some glm thickness analyses!
>
>
>
> Currently I am doing a thickness analysis looking at the difference
> between two groups while controlling for age, and two continuous measures
> of depression and anxiety. The general commands I run are as follows:
>
>
>
> mris_preproc --fsgd [fsgd filename] --cache-in thickness.fwhm10.fsaverage
> --target fsaverage --hemi lh --o lh.[filename].thickness.10.mgh
>
> mris_preproc --fsgd [fsgd filename] --cache-in thickness.fwhm10.fsaverage
> --target fsaverage --hemi rh --o rh.[filename].thickness.10.mgh
>
> mri_glmfit --y lh.[filename].thickness.10.mgh --fsgd [fsgd filename] doss
> --C contrast.mtx --surf fsaverage lh --glmdir lh_[filename]_fwhm10.glmdir
>
> mri_glmfit --y rh.[filename].thickness.10.mgh --fsgd [fsgd filename] doss
> --C contrast.mtx --surf fsaverage rh --glmdir rh_[filename]_fwhm10.glmdir
>
> mri_glmfit-sim --glmdir lh_[filename]_fwhm10.glmdir --cwpvalthresh .05
> --cache 2.0 abs --2spaces
>
> mri_glmfit-sim --glmdir rh_[filename]_fwhm10.glmdir --cwpvalthresh .05
> --cache 2.0 abs --2spaces
>
>
>
> I noticed that in some analyses there would be no significant clusters
> when the threshold is set at 2.0 (p<0.01) but if you were to run the same
> analyses with a threshold at 2.3 (p<0.005) there would be a significant
> cluster, in the lingual for example. If I go one step further and set the
> threshold to 3.0 there is also a significant cluster – however the cluster
> is now in the isthmuscingulate.
>
>
>
> Am I doing something incorrectly or is this possible? And if so, could you
> help me understand what is going on here.
>
>
>
> Best,
>
>
>
> Andrew
>
>
>
>
> ___
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[Freesurfer] mri_glmfit-sim - Clusterwise correction for multiple comparisons.

[Guthrie, Andrew J.]

External Email - Use Caution

Hi all,

I took the freesurfer course in the recent past, and I am now beginning to run 
some glm thickness analyses!

Currently I am doing a thickness analysis looking at the difference between two 
groups while controlling for age, and two continuous measures of depression and 
anxiety. The general commands I run are as follows:

mris_preproc --fsgd [fsgd filename] --cache-in thickness.fwhm10.fsaverage 
--target fsaverage --hemi lh --o lh.[filename].thickness.10.mgh
mris_preproc --fsgd [fsgd filename] --cache-in thickness.fwhm10.fsaverage 
--target fsaverage --hemi rh --o rh.[filename].thickness.10.mgh
mri_glmfit --y lh.[filename].thickness.10.mgh --fsgd [fsgd filename] doss --C 
contrast.mtx --surf fsaverage lh --glmdir lh_[filename]_fwhm10.glmdir
mri_glmfit --y rh.[filename].thickness.10.mgh --fsgd [fsgd filename] doss --C 
contrast.mtx --surf fsaverage rh --glmdir rh_[filename]_fwhm10.glmdir
mri_glmfit-sim --glmdir lh_[filename]_fwhm10.glmdir --cwpvalthresh .05 --cache 
2.0 abs --2spaces
mri_glmfit-sim --glmdir rh_[filename]_fwhm10.glmdir --cwpvalthresh .05 --cache 
2.0 abs --2spaces

I noticed that in some analyses there would be no significant clusters when the 
threshold is set at 2.0 (p<0.01) but if you were to run the same analyses with 
a threshold at 2.3 (p<0.005) there would be a significant cluster, in the 
lingual for example. If I go one step further and set the threshold to 3.0 
there is also a significant cluster - however the cluster is now in the 
isthmuscingulate.

Am I doing something incorrectly or is this possible? And if so, could you help 
me understand what is going on here.

Best,

Andrew


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Re: [Freesurfer] mri_glmfit-sim cluster output issue

[Douglas N. Greve]

   External Email - Use Caution

which part do you want to fix? the command not found or the lack of 
clusters?


On 6/28/2023 6:25 PM, jordan wagner wrote:


External Email - Use Caution

Hello,

My name is Jordan and I am working on cluster correction between two 
groups. I ran the step before: "freeview -f 
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=sig.mgh". I was able 
to find many significant values of p<0.05. However, when I ran the 
cluster correction there were no significant cluster in any of my 
group comparisons. I had to run mri_glmit-sim in the terminal each 
time for every directory because running the script that looped 
resulted in "cwp: command not found".


I was wondering if there is something I could look for that is causing 
an issue or something else I can do to fix this. I wanted to reach out 
to make sure my results aren't completely null.


Thank you,
Jordan Wagner

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[Freesurfer] mri_glmfit-sim cluster output issue

[jordan wagner]

External Email - Use Caution

Hello,

My name is Jordan and I am working on cluster correction between two
groups. I ran the step before: "freeview -f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=sig.mgh". I was able to
find many significant values of p<0.05. However, when I ran the cluster
correction there were no significant cluster in any of my group
comparisons. I had to run mri_glmit-sim in the terminal each time for every
directory because running the script that looped resulted in "cwp: command
not found".

I was wondering if there is something I could look for that is causing an
issue or something else I can do to fix this. I wanted to reach out to make
sure my results aren't completely null.

Thank you,
Jordan Wagner
___
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Re: [Freesurfer] mri_glmfit correction across lobes

[Douglas N. Greve]

You can, but you need to give mri_glmfit the specific label to use as a 
mask (eg, --label or --mask). You can extract labels from an annot with 
mri_annotation2label. Then mri_glmfit-sim will automatically restrict 
the correction to that label


On 4/6/2023 10:05 AM, John Anderson wrote:


External Email - Use Caution

Dear Dr Greve,
Apologize for not providing a clear explanation earlier. The file 
lh.all.suvr.sm05.proj0.5.nii.gz is the result of combining all SUVR 
maps, using mri_concat, after projecting them onto the brain surface 
with mri_vol2surf.
I would like to know if it is possible to use mri_glmfit-sim to 
correct for specific regions of interest (such as lobes) instead of 
correcting the entire brain.
I am using the following command: mri_glmfit-sim --glmdir 
lh.suvr.glmdir --cache 4 pos --cwp 0.05 --2spaces


When I include the "--annot lobes" option in my command 
(mri_glmfit-sim --glmdir lh.suvr.glmdir --cache 4 pos --cwp 0.05 
--2spaces --annot lobes), the resulting statistical output is similar, 
but the annotations are replaced with their corresponding lobes. 
However, p-values are not adjusted for the number of regions of 
interest specified in the "--annot" option. Thanks again


On Wed, Apr 5, 2023 at 10:46 PM Douglas N. Greve 
 wrote:


What is h.all.suvr.sm05.proj0.5.nii.gz? Where did it come from?
The name looks like it might be a voxel-wise map, but you say
something about ROIs. mri_glmfit does not correct for multiple
comparisons. For ROI-based analyses, you can use bonferroni or
FDR. For maps you can use mri_glmfit-sim.

On 4/4/2023 4:53 PM, John Anderson wrote:


External Email - Use Caution

Hello Freesurfer,
Currently, I am using the Petsurfer manual, which is easily
understandable and clear. Nonetheless, I have a question
regarding the "mri_glmfit" step.
As far as I know, this command is used to correct data for
multiple comparisons among all the ROIs in the aparc+aseg.mgz
file. Can you please confirm if my understanding is correct?

mri_glmfit.bin --y lh.all.suvr.sm05.proj0.5.nii.gz --fsgd
2G0C.fsgd --C patients_vs_controls.mtx --surf fsaverage lh
--cortex --glmdir lh.patinets_vs_controls

In particular, I am interested in correcting data across lobes
instead of across all ROIs. I followed the steps mentioned in the
FS forum to create lobes, and I can observe lobe annotations in
the wmparc.mgz file. I am curious to know whether using the
"--annot" flag will adjust the p-values across different lobe
ROIs instead of all ROIs in the aparc+aseg.mgz file. I have
attempted this, but it appears to only change the name of the
annotation in the final statistics file, and the p-value remains
the same. Do I need to include any additional arguments in the
command?

Thanks for your help
John

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Re: [Freesurfer] mri_glmfit correction across lobes

[John Anderson]

External Email - Use Caution

Dear Dr Greve,
Apologize for not providing a clear explanation earlier. The file
lh.all.suvr.sm05.proj0.5.nii.gz is the result of combining all SUVR maps,
using mri_concat, after projecting them onto the brain surface with
mri_vol2surf.
I would like to know if it is possible to use mri_glmfit-sim to correct for
specific regions of interest (such as lobes) instead of correcting the
entire brain.
I am using the following command: mri_glmfit-sim --glmdir lh.suvr.glmdir
--cache 4 pos --cwp 0.05 --2spaces

When I include the "--annot lobes" option in my command (mri_glmfit-sim
--glmdir lh.suvr.glmdir --cache 4 pos --cwp 0.05 --2spaces --annot lobes),
the resulting statistical output is similar, but the annotations are
replaced with their corresponding lobes. However, p-values are not adjusted
for the number of regions of interest specified in the "--annot" option.
Thanks again

On Wed, Apr 5, 2023 at 10:46 PM Douglas N. Greve 
wrote:

> What is h.all.suvr.sm05.proj0.5.nii.gz? Where did it come from? The name
> looks like it might be a voxel-wise map, but you say something about ROIs.
> mri_glmfit does not correct for multiple comparisons. For ROI-based
> analyses, you can use bonferroni or FDR. For maps you can use
> mri_glmfit-sim.
>
> On 4/4/2023 4:53 PM, John Anderson wrote:
>
> External Email - Use Caution
> Hello Freesurfer,
> Currently, I am using the Petsurfer manual, which is easily understandable
> and clear. Nonetheless, I have a question regarding the "mri_glmfit" step.
> As far as I know, this command is used to correct data for multiple
> comparisons among all the ROIs in the aparc+aseg.mgz file. Can you please
> confirm if my understanding is correct?
>
> mri_glmfit.bin --y lh.all.suvr.sm05.proj0.5.nii.gz --fsgd 2G0C.fsgd --C
> patients_vs_controls.mtx --surf fsaverage lh --cortex --glmdir
> lh.patinets_vs_controls
>
> In particular, I am interested in correcting data across lobes instead of
> across all ROIs. I followed the steps mentioned in the FS forum to create
> lobes, and I can observe lobe annotations in the wmparc.mgz file. I am
> curious to know whether using the "--annot" flag will adjust the p-values
> across different lobe ROIs instead of all ROIs in the aparc+aseg.mgz file.
> I have attempted this, but it appears to only change the name of the
> annotation in the final statistics file, and the p-value remains the same.
> Do I need to include any additional arguments in the command?
>
> Thanks for your help
> John
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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>
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Re: [Freesurfer] mri_glmfit correction across lobes

[Douglas N. Greve]

What is h.all.suvr.sm05.proj0.5.nii.gz? Where did it come from? The name 
looks like it might be a voxel-wise map, but you say something about 
ROIs. mri_glmfit does not correct for multiple comparisons. For 
ROI-based analyses, you can use bonferroni or FDR. For maps you can use 
mri_glmfit-sim.


On 4/4/2023 4:53 PM, John Anderson wrote:


External Email - Use Caution

Hello Freesurfer,
Currently, I am using the Petsurfer manual, which is easily 
understandable and clear. Nonetheless, I have a question regarding the 
"mri_glmfit" step.
As far as I know, this command is used to correct data for multiple 
comparisons among all the ROIs in the aparc+aseg.mgz file. Can you 
please confirm if my understanding is correct?


mri_glmfit.bin --y lh.all.suvr.sm05.proj0.5.nii.gz --fsgd 2G0C.fsgd 
--C patients_vs_controls.mtx --surf fsaverage lh --cortex --glmdir 
lh.patinets_vs_controls


In particular, I am interested in correcting data across lobes instead 
of across all ROIs. I followed the steps mentioned in the FS forum to 
create lobes, and I can observe lobe annotations in the wmparc.mgz 
file. I am curious to know whether using the "--annot" flag will 
adjust the p-values across different lobe ROIs instead of all ROIs in 
the aparc+aseg.mgz file. I have attempted this, but it appears to only 
change the name of the annotation in the final statistics file, and 
the p-value remains the same. Do I need to include any additional 
arguments in the command?


Thanks for your help
John

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contains patient information, please contact the Mass General Brigham 
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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] mri_glmfit correction across lobes

[John Anderson]

External Email - Use Caution

Hello Freesurfer,
Currently, I am using the Petsurfer manual, which is easily understandable
and clear. Nonetheless, I have a question regarding the "mri_glmfit" step.
As far as I know, this command is used to correct data for multiple
comparisons among all the ROIs in the aparc+aseg.mgz file. Can you please
confirm if my understanding is correct?

mri_glmfit.bin --y lh.all.suvr.sm05.proj0.5.nii.gz --fsgd 2G0C.fsgd --C
patients_vs_controls.mtx --surf fsaverage lh --cortex --glmdir
lh.patinets_vs_controls

In particular, I am interested in correcting data across lobes instead of
across all ROIs. I followed the steps mentioned in the FS forum to create
lobes, and I can observe lobe annotations in the wmparc.mgz file. I am
curious to know whether using the "--annot" flag will adjust the p-values
across different lobe ROIs instead of all ROIs in the aparc+aseg.mgz file.
I have attempted this, but it appears to only change the name of the
annotation in the final statistics file, and the p-value remains the same.
Do I need to include any additional arguments in the command?

Thanks for your help
John
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 .
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] mri_glmfit error - matrix ill-conditioned. no solution from archive.

[Douglas N. Greve]

The scale is much different between columns 1 and 8, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.

On 3/21/2023 1:53 PM, miracle ozzoude wrote:


External Email - Use Caution

Hello,

Any idea how to solve this problem? I have tried the suggested 
solutions on the archive, that's Demean and Rescale but to no avail.


I have attached the necessary files in the email below.

Many thanks,
Miracle

mri_glmfit command: mri_glmfit --y 
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh 
--fsgd thickness_DHI_Emotional_edit.fsgd dods --C thickness_edit.mtx 
--surf fsaverage lh --cortex --glmdir 
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir


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 .
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Re: [Freesurfer] mri_glmfit-sim error

[Douglas N. Greve]

Yes, all the 7.X versions will give the same answer unless you 
explicitly use a new feature


On 3/20/2023 2:45 PM, mariangela asimina wrote:


External Email - Use Caution

I see now this is an issue addressed stable 7.2.0 version of FreeSurfer:
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes 
<https://secure-web.cisco.com/1_0nM8kQPAwlCZzUFPKYxFeyxAfrBfjVnMbuFBgpiLtOtAz0Rcg2ns0AHK0Z-UuAC0K-jylD0ZM1hP4emJWrKoCvyUwJv4VVaznUFGMKUwg5OuApejYTaxHdKuzNe5HOOGskw2aVkgC0HOeyCPniLzoA5MSfRjpv1RfRJdNli3dKvwIjsY48WuxJT69HBkSXeu374bWB2rlhnP3OpNcmqdmIzR2dm46aiVRBcm3JvbkQLgtvhZeadmj2hfxQUQPDJYVfkQcP70pazbHOft-_rcNzvPKYmvvAAelzNeTuwNBoa1gQT-rqipRmHUXA8AhgFoON7c7sEJ06rpAXxn2QgBw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes>


mri_glmfit-sim

  * Fixed locale issue to handle cases where decimal points are
represented by commas.


Is it ok to install the newest version (7.3.2) and run mri_glmfit-sim 
on data made with the version I used?
Is it ok to troubleshoot the recon-all output that I already have, 
after installing the newer version? Or would I have to run the 
recon-all again?


Lastly, if the answer to the above is negative, is it possible to 
solve the issue with the commas on the version I am using?


Thank you!
Mariangela




*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of mariangela 
asimina 

*Sent:* Monday, March 20, 2023 8:13 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* [Freesurfer] mri_glmfit-sim error

External Email - Use Caution

Hello FreeSurfer developers and experts,

I am trying to do cluster correction with mri_glmfit-sim after running 
mri_glmfit.


The command I ran:
  mri_glmfit-sim --glmdir lh.volume.SCNStudyTest.10.glmdir --cache 
3.0 abs --cwp 0.05 --2spaces


produces the following error:
  ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0

FreeSurfer version: 
freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b

Operating System: Ubuntu 22.04.2 LTS
Kernel: Linux 5.19.0-35-generic


I have searched the archive and cannot find a similar error.
I would appreciate your help.


Mariangela Asimina


I also ran the command with the --debug flag and I get the following 
output, but I'm afraid I can't interpret it:

set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 8 != 0 )

set flag = $argv[1] ; shift ;
set flag = --glmdir
shift

switch ( $flag )
switch ( --glmdir )
if ( $#argv < 0 ) goto arg1err ;
if ( 7 < 0 ) goto arg1err
set glmdir = $argv[1] ; shift ;
set glmdir = lh.volume.SCNStudyTest.10.glmdir
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 6 != 0 )

set flag = $argv[1] ; shift ;
set flag = --cache
shift

switch ( $flag )
switch ( --cache )
if ( $#argv < 2 ) goto arg2err ;
if ( 5 < 2 ) goto arg2err
set thresh = $argv[1] ; shift ;
set thresh = 3.0
shift
set simsign = $argv[1] ; shift ;
set simsign = abs
shift
set UseCache = 1 ;
set UseCache = 1
set DoSim = 0 ;
set DoSim = 0

set thresh = `echo $thresh | sed 's/,/./g'`
set thresh = `echo $thresh | sed 's/,/./g'`
sed s/,/./g
echo 3.0
set thresh = `printf %2.1f $thresh`
set thresh = `printf %2.1f $thresh`
printf %2.1f 3.0
if ( $thresh != 1.3 && $thresh != 2.0 && $thresh != 2.3 && $thresh != 
3.0 && $thresh != 3.3 && $thresh != 4.0 ) then
if ( 3,0 != 1.3 && 3,0 != 2.0 && 3,0 != 2.3 && 3,0 != 3.0 && 3,0 != 
3.3 && 3,0 != 4.0 ) then

echo "ERROR: thresh = $thresh, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0"
echo ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
exit 1 ;
exit 1


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The information in this e-mail is intended only for the person to whom it is 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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[Freesurfer] mri_glmfit error - matrix ill-conditioned. no solution from archive.

[miracle ozzoude]

External Email - Use Caution

Hello,

Any idea how to solve this problem? I have tried the suggested solutions on
the archive, that's Demean and Rescale but to no avail.

I have attached the necessary files in the email below.

Many thanks,
Miracle

mri_glmfit command: mri_glmfit --y
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh
--fsgd thickness_DHI_Emotional_edit.fsgd dods --C thickness_edit.mtx --surf
fsaverage lh --cortex --glmdir
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir
bash-3.2$ mri_glmfit --y 
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh 
--fsgd thickness_DHI_Emotional_edit.fsgd dods --C thickness_edit.mtx --surf 
fsaverage lh --cortex --glmdir 
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir
gdfRead(): reading thickness_DHI_Emotional_edit.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 47.0476 9.22459
1 Sports 0.619048 1.13289
2 Days_TBI 1734.1 919.571
3 Emotional 13.5238 7.19536
Class Size and Means of each Continuous Variable
1 PPCS_male  5  39.8000   1.6000 1557.8000  12.8000 
2 PPCS_female 16  49.3125   0.3125 1789.1875  13.7500 
WARNING: Class PPCS_male has 5 members. With 4 variables and using DODS, This 
is the bare minimum which may cause problems with the design matrix.
INFO: gd2mtx_method is dods
Reading source surface 
/Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 65417.00
AvgVtxArea   0.399269
AvgVtxDist   0.721953
StdVtxDist   0.195472

7.2.0
cwd /Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness
cmdline mri_glmfit --y 
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh 
--fsgd thickness_DHI_Emotional_edit.fsgd dods --C thickness_edit.mtx --surf 
fsaverage lh --cortex --glmdir 
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir 
sysname  Darwin
hostname ip-130-63-40-126.dynamic.yorku.ca
machine  x86_64
user sergiolab
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
/Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness/results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh
logyflag 0
usedti  0
FSGD thickness_DHI_Emotional_edit.fsgd
labelmask  
/Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness/fsaverage/label/lh.cortex.label
maskinv 0
glmdir results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory 
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir
Loading y from 
/Users/sergiolab/Documents/Miracle/Analysis/Cortical_thickness/results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh
   ... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to 
results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 653034
Design matrix --
 1.0   0.0   30.0   0.0   4.0   0.0   1687.0   
0.0   10.0   0.0;
 0.0   1.0   0.0   46.0   0.0   0.0   0.0   
2149.0   0.0   12.0;
 1.0   0.0   41.0   0.0   0.0   0.0   2148.0   
0.0   6.0   0.0;
 0.0   1.0   0.0   49.0   0.0   0.0   0.0   
2257.0   0.0   18.0;
 0.0   1.0   0.0   51.0   0.0   0.0   0.0   
1939.0   0.0   28.0;
 0.0   1.0   0.0   61.0   0.0   0.0   0.0   
3404.0   0.0   8.0;
 0.0   1.0   0.0   53.0   0.0   0.0   0.0   
2368.95825   0.0   6.0;
 0.0   1.0   0.0   60.0   0.0   2.0   0.0   
1407.0   0.0   10.0;
 0.0   1.0   0.0   48.0   0.0   0.0   0.0   
1670.95837   0.0   6.0;
 0.0   1.0   0.0   38.0   0.0   0.0   0.0   
12.0   0.0   26.0;
 0.0   1.0   0.0   63.0   0.0   0.0   0.0   
796.0   0.0   18.0;
 0.0   1.0   0.0   40.0   0.0   0.0   0.0   
476.0   0.0   6.0;
 0.0   1.0   0.0   44.0   0.0   2.0   0.0   
1980.0   0.0   14.0;
 0.0   1.0   0.0   50.0   0.0   1.0   0.0   
3517.04175   0.0   6.0;
 1.0   0.0   29.0   0.0   1.0   0.0   177.04167   
0.0   18.0   0.0;
 0.0   1.0   0.0   39.0   0.0   0.0   0.0   
2571.0   0.0   22.0;
 0.0   1.0   0.0   53.0   0.0   0.0   0.0   
1872.0   0.0   18.0;
 1.0   0.0   59.0   0.0   0.0   0.0   1148.0   
0.0   24.0   0.0;
 

Re: [Freesurfer] mri_glmfit-sim error

[mariangela asimina]

External Email - Use Caution

I see now this is an issue addressed stable 7.2.0 version of FreeSurfer:
https://secure-web.cisco.com/1_0nM8kQPAwlCZzUFPKYxFeyxAfrBfjVnMbuFBgpiLtOtAz0Rcg2ns0AHK0Z-UuAC0K-jylD0ZM1hP4emJWrKoCvyUwJv4VVaznUFGMKUwg5OuApejYTaxHdKuzNe5HOOGskw2aVkgC0HOeyCPniLzoA5MSfRjpv1RfRJdNli3dKvwIjsY48WuxJT69HBkSXeu374bWB2rlhnP3OpNcmqdmIzR2dm46aiVRBcm3JvbkQLgtvhZeadmj2hfxQUQPDJYVfkQcP70pazbHOft-_rcNzvPKYmvvAAelzNeTuwNBoa1gQT-rqipRmHUXA8AhgFoON7c7sEJ06rpAXxn2QgBw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes


mri_glmfit-sim

  *   Fixed locale issue to handle cases where decimal points are represented 
by commas.

Is it ok to install the newest version (7.3.2) and run mri_glmfit-sim on data 
made with the version I used?
Is it ok to troubleshoot the recon-all output that I already have, after 
installing the newer version? Or would I have to run the recon-all again?

Lastly, if the answer to the above is negative, is it possible to solve the 
issue with the commas on the version I am using?

Thank you!
Mariangela




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of mariangela asimina 

Sent: Monday, March 20, 2023 8:13 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] mri_glmfit-sim error


External Email - Use Caution

Hello FreeSurfer developers and experts,

I am trying to do cluster correction with mri_glmfit-sim after running 
mri_glmfit.

The command I ran:
  mri_glmfit-sim --glmdir lh.volume.SCNStudyTest.10.glmdir --cache 3.0 abs 
--cwp 0.05 --2spaces

produces the following error:
  ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0

FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
Operating System: Ubuntu 22.04.2 LTS
Kernel: Linux 5.19.0-35-generic


I have searched the archive and cannot find a similar error.
I would appreciate your help.


Mariangela Asimina


I also ran the command with the --debug flag and I get the following output, 
but I'm afraid I can't interpret it:
set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 8 != 0 )

set flag = $argv[1] ; shift ;
set flag = --glmdir
shift

switch ( $flag )
switch ( --glmdir )
if ( $#argv < 0 ) goto arg1err ;
if ( 7 < 0 ) goto arg1err
set glmdir = $argv[1] ; shift ;
set glmdir = lh.volume.SCNStudyTest.10.glmdir
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 6 != 0 )

set flag = $argv[1] ; shift ;
set flag = --cache
shift

switch ( $flag )
switch ( --cache )
if ( $#argv < 2 ) goto arg2err ;
if ( 5 < 2 ) goto arg2err
set thresh = $argv[1] ; shift ;
set thresh = 3.0
shift
set simsign = $argv[1] ; shift ;
set simsign = abs
shift
set UseCache = 1 ;
set UseCache = 1
set DoSim = 0 ;
set DoSim = 0

set thresh = `echo $thresh | sed 's/,/./g'`
set thresh = `echo $thresh | sed 's/,/./g'`
sed s/,/./g
echo 3.0
set thresh = `printf %2.1f $thresh`
set thresh = `printf %2.1f $thresh`
printf %2.1f 3.0
if ( $thresh != 1.3 && $thresh != 2.0 && $thresh != 2.3 && $thresh != 3.0 && 
$thresh != 3.3 && $thresh != 4.0 ) then
if ( 3,0 != 1.3 && 3,0 != 2.0 && 3,0 != 2.3 && 3,0 != 3.0 && 3,0 != 3.3 && 3,0 
!= 4.0 ) then
echo "ERROR: thresh = $thresh, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0"
echo ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
exit 1 ;
exit 1

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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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[Freesurfer] mri_glmfit-sim error

[mariangela asimina]

External Email - Use Caution

Hello FreeSurfer developers and experts,

I am trying to do cluster correction with mri_glmfit-sim after running 
mri_glmfit.

The command I ran:
  mri_glmfit-sim --glmdir lh.volume.SCNStudyTest.10.glmdir --cache 3.0 abs 
--cwp 0.05 --2spaces

produces the following error:
  ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0

FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
Operating System: Ubuntu 22.04.2 LTS
Kernel: Linux 5.19.0-35-generic


I have searched the archive and cannot find a similar error.
I would appreciate your help.


Mariangela Asimina


I also ran the command with the --debug flag and I get the following output, 
but I'm afraid I can't interpret it:
set echo = 1 ;
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 8 != 0 )

set flag = $argv[1] ; shift ;
set flag = --glmdir
shift

switch ( $flag )
switch ( --glmdir )
if ( $#argv < 0 ) goto arg1err ;
if ( 7 < 0 ) goto arg1err
set glmdir = $argv[1] ; shift ;
set glmdir = lh.volume.SCNStudyTest.10.glmdir
shift
breaksw
breaksw

end
end
while ( $#argv != 0 )
while ( 6 != 0 )

set flag = $argv[1] ; shift ;
set flag = --cache
shift

switch ( $flag )
switch ( --cache )
if ( $#argv < 2 ) goto arg2err ;
if ( 5 < 2 ) goto arg2err
set thresh = $argv[1] ; shift ;
set thresh = 3.0
shift
set simsign = $argv[1] ; shift ;
set simsign = abs
shift
set UseCache = 1 ;
set UseCache = 1
set DoSim = 0 ;
set DoSim = 0

set thresh = `echo $thresh | sed 's/,/./g'`
set thresh = `echo $thresh | sed 's/,/./g'`
sed s/,/./g
echo 3.0
set thresh = `printf %2.1f $thresh`
set thresh = `printf %2.1f $thresh`
printf %2.1f 3.0
if ( $thresh != 1.3 && $thresh != 2.0 && $thresh != 2.3 && $thresh != 3.0 && 
$thresh != 3.3 && $thresh != 4.0 ) then
if ( 3,0 != 1.3 && 3,0 != 2.0 && 3,0 != 2.3 && 3,0 != 3.0 && 3,0 != 3.3 && 3,0 
!= 4.0 ) then
echo "ERROR: thresh = $thresh, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0"
echo ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0
exit 1 ;
exit 1

___
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Freesurfer@nmr.mgh.harvard.edu
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] mri_glmfit with age-squared

[Douglas N. Greve]

It is probably a scaling problem with using age^2. Try normalizing the 
age^2 column (ie, remove the mean and divide by the sum of the squares)


On 3/9/2023 3:30 PM, Triebswetter, Curtis wrote:


External Email - Use Caution

Hello Freesurfer experts,

I am attempting to run the command

mri_glmfit --y lh.RBS_ADRC_N0_control.10.mgh --fsgd 
RBS_ADRC_APOE_age22.fsgd dods --C APOE_ageINT.mtx  --surf fsaverage lh 
--cortex --glmdir lh.RBS_ADRC_N0.glmdir


On this .fsgd file:

“RBS_ADRC_APOE_age22.txt”

Using the following design matrix:

“lh.RBS_ADRC_N0.txt”

I am receiving the error message:



ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08



Possible problem with experimental design:

Check for duplicate entries and/or lack of range of

continuous variables within a class.

I would appreciate your insights into what may be the likely cause of 
this error and apologize that the files are in text format. If need 
be, I can convert these to their proper formats.


misc information:

Freesurfer 6.00

CentOS v7

Best,

Curtis


___
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Freesurfer@nmr.mgh.harvard.edu
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___
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
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[Freesurfer] mri_glmfit with age-squared

[Triebswetter, Curtis]

External Email - Use Caution

Hello Freesurfer experts,

I am attempting to run the command
mri_glmfit --y lh.RBS_ADRC_N0_control.10.mgh --fsgd RBS_ADRC_APOE_age22.fsgd 
dods --C APOE_ageINT.mtx  --surf fsaverage lh --cortex --glmdir 
lh.RBS_ADRC_N0.glmdir

On this .fsgd file:
“RBS_ADRC_APOE_age22.txt”

Using the following design matrix:

“lh.RBS_ADRC_N0.txt”

I am receiving the error message:

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.

I would appreciate your insights into what may be the likely cause of this 
error and apologize that the files are in text format. If need be, I can 
convert these to their proper formats.

misc information:
Freesurfer 6.00
CentOS v7


Best,
Curtis
GroupDescriptorFile 1
Title RBS_ADRC_APOE_age2_sex_control
Class FE4neg1
Class FE4pos1
Class FE4neg2
Class FE4pos2
Class ME4neg1
Class ME4pos1
Class ME4neg2
Class ME4pos2
Variables Age Age2
Input   FSURF_RBS01LJ00635_20150619_121551_20150619.121551_1FE4pos1 
-1.3167308791.733780208
Input   FSURF_RBS01LJ04931_20140410_123922_20140410.123922_1FE4pos1 
-5.21673087927.21428106
Input   FSURF_RBS01LJ05491_20150522_120949_20150522.120949_1FE4pos1 
11.88326912 141.212085
Input   FSURF_RBS01LJ00357_20140528_123655_20140528.123655_1FE4neg1 
-5.61673087931.54766577
Input   FSURF_RBS01LJ02140_20140612_121718_20140612.121718_1FE4neg1 
-5.71673087932.68101194
Input   FSURF_RBS01LJ03496_20140812_121641_20140812.121641_1FE4neg1 
-0.7167308790.513703153
Input   FSURF_RBS01LJ04399_20150624_115927_20150624.115927_1FE4neg1 
3.083269121 9.506548473
Input   FSURF_RBS01LJ04474_20140710_121401_20140710.121401_1FE4neg1 
-3.31673087911.00070372
Input   FSURF_RBS01LJ04692_20140910_124909_20140910.124909_1FE4neg1 
-2.4167308795.840588141
Input   FSURF_RBS01LJ04841_20150107_121028_20150107.121028_1FE4neg1 
8.183269121 66.96589351
Input   FSURF_ADRC3047_20150204_161246_20150204.161246_1FE4neg1 
-11.21673088125.8150516
Input   FSURF_ADRC3537_20150415_141949_20150415.141949_1FE4neg1 
3.783269121 14.31312524
Input   FSURF_RBS01LJ02603_20151007_121518_20151007.121518_1FE4pos1 
8.483269121 71.96585498
Input   FSURF_RBS01LJ03097_20151209_120245_20151209.120245_1FE4pos1 
10.08326912 101.6723162
Input   FSURF_RBS01LJ03591_20140820_124751_20140820.124751_1FE4pos1 
-3.51673087912.36739608
Input   FSURF_RBS01LJ03597_20160323_120518_20160323.120518_1FE4pos1 
3.983269121 15.86643289
Input   FSURF_RBS01LJ04191_20160527_120933_20160527.120933_1FE4pos1 
-4.31673087918.63416548
Input   FSURF_RBS01LJ04226_20150114_121418_20150114.121418_1FE4pos1 
-0.8167308790.667049329
Input   FSURF_RBS01LJ04471_20150902_123724_20150902.123724_1FE4pos1 
0.783269121 0.613510516
Input   FSURF_RBS01LJ04972_20160608_105227_20160608.105227_1FE4pos1 
5.183269121 26.86627878
Input   FSURF_RBS01LJ05204_20150923_120105_20150923.120105_1FE4pos1 
-1.0167308791.03374168
Input   FSURF_RBS01LJ06014_20150612_115706_20150612.115706_1FE4pos1 
-3.21673087910.34735755
Input   FSURF_RBS01LJ06333_20150821_115630_20150821.115630_1FE4pos1 
5.683269121 32.2995479
Input   FSURF_140116cw015_20140116_095920_20140116.095920_1 FE4pos1 
-7.21673087952.08120458
Input   FSURF_140716cw019_20140716_103307_20140716.103307_1 FE4pos1 
-3.21673087910.34735755
Input   FSURF_150430cw025_20150430_121606_20150430.121606_1 FE4pos1 
-8.21673087967.51466634
Input   FSURF_ADRC3351_20170522_124419_20170522.124419_1FE4pos1 
0.783269121 0.613510516
Input   FSURF_ADRC3383_20130425.100851_1FE4pos1 3.783269121 
14.31312524
Input   FSURF_ADRC3564_20170713_101052_20170713.101052_1FE4pos1 
-1.2167308791.480434032
Input   FSURF_ADRC3572_20170605_115303_20170605.115303_1FE4pos1 
-6.21673087938.64774282
Input   FSURF_ADRC3748_20210702_115232_20210702.115232_1FE4pos2 
-1.9167308793.673857262
Input   FSURF_ADRC3828_20201102_145018_20201102.145018_1FE4pos2 
-3.91673087915.34078078
Input   FSURF_ADRC3834_20201027_143411_20201027.143411_1FE4pos2 
-2.3167308795.367241966
Input   FSURF_ADRC8092_20130418.111516_1FE4pos1 1.783269121 
3.180048758
Input   FSURF_RBSBDV100155_20150715_120042_20150715.120042_1FE4pos1 
13.18326912 173.7985847
Input   FSURF_RBSBDV100193_20150506_111413_20150506.111413_1FE4pos1 
12.28326912 150.8787003
Input   FSURF_RBSD1LJ00018_20160713_115259_20160713.115259_1FE4pos1 
-15.51673088240.7689372
Input   FSURF_RBSR02J00518_20160525_122715_20160525.122715_1FE4pos1 
-3.61673087913.08074225
Input   FSURF_RBSV1LJ00507_20160127_115959_20160127.115959_1FE4pos1 
10.2832

Re: [Freesurfer] mri_glmfit

[Douglas N. Greve]

James, what do you mean by restrict the analysis within lobes? An ROI 
analysis? Adding --label will not give you an ROI analysis.


On 1/20/2023 9:32 AM, Huang, Yujing wrote:


Hi James,

Did mri_annotation2label commands create lh.lobes.annot and 
rh.lobes.annot in fsaverage/labels directory?


They are annot files. You can use mri_annotation2label to break them 
into label files.


Best,

Yujing

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 *On Behalf Of *James Brown

*Sent:* Thursday, January 19, 2023 7:19 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* [Freesurfer] mri_glmfit

*External Email - Use Caution *

Dear FS experts,

I am working on a surface based analysis using FS 7.1.1 and I would 
like to run mri_glmfit between two groups using the flag "--label" to 
restrict analysis within lobes.


I ran these commands on fsaverage

mri_annotation2label --subject fsaverage --hemi lh --lobesStrict lobes
mri_annotation2label --subject fsaverage --hemi rh --lobesStrict lobes

This created annotation files within the "labels"  folder of 
fsaverage, then I ran mri_glmfit using the flag --label lh.lobes from 
fsaverage


I got this error message

mri_glmfit: could not scan # of lines from label file

I am ot sure what I am doing wrong. Thanks for guidance


James


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Re: [Freesurfer] mri_glmfit

[Huang, Yujing]

Hi James,

Did mri_annotation2label commands create lh.lobes.annot and rh.lobes.annot in 
fsaverage/labels directory?

They are annot files. You can use mri_annotation2label to break them into label 
files.

Best,

Yujing




From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of James Brown
Sent: Thursday, January 19, 2023 7:19 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_glmfit


External Email - Use Caution
Dear FS experts,
I am working on a surface based analysis using FS 7.1.1 and I would like to run 
mri_glmfit between two groups using the flag "--label" to restrict analysis 
within lobes.

I ran these commands on fsaverage

mri_annotation2label --subject fsaverage --hemi lh --lobesStrict lobes
mri_annotation2label --subject fsaverage --hemi rh --lobesStrict lobes

This created annotation files within the "labels"  folder of fsaverage, then I 
ran mri_glmfit using the flag --label lh.lobes from fsaverage

I got this error message
mri_glmfit: could not scan # of lines from label file

I am ot sure what I am doing wrong. Thanks for guidance

James
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[Freesurfer] mri_glmfit

[James Brown]

External Email - Use Caution

Dear FS experts,
I am working on a surface based analysis using FS 7.1.1 and I would like to
run mri_glmfit between two groups using the flag "--label" to restrict
analysis within lobes.

I ran these commands on fsaverage

mri_annotation2label --subject fsaverage --hemi lh --lobesStrict lobes
mri_annotation2label --subject fsaverage --hemi rh --lobesStrict lobes

This created annotation files within the "labels"  folder of fsaverage,
then I ran mri_glmfit using the flag --label lh.lobes from fsaverage

I got this error message
mri_glmfit: could not scan # of lines from label file

I am ot sure what I am doing wrong. Thanks for guidance

James
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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 .
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Re: [Freesurfer] mri_glmfit with doss isn't working. v7.2

[miracle ozzoude]

External Email - Use Caution

Hello Doug,

Do you mean like this?

GroupDescriptorFile 1

Title Rivermead cluster 2

DOSS

Class PPCS_Male

Class PPCS_Female

Variables Age Sports Games Days_TBI RPQ_13


If yes, i did but still getting similar area


Best,

Paul

On Tue, Jan 3, 2023 at 11:51 AM miracle ozzoude 
wrote:

> Hello Doug,
>
> Thanks for the quick response. I did see the error. However, I specified
> doss in the mri_glmfit command and my mtx looks accurate as indicated
> above. Does that mean it can only work with dods? The reason I'm using 2
> groups is because I want to regress out the effect of sex. However, the
> recommended way to do it in fsgd is to create a class for it and I only
> have 3 males.
>
> Is there a workaround for this?
>
> Many thanks.
>
> On Fri, Dec 30, 2022 at 6:37 PM miracle ozzoude 
> wrote:
>
>> Hello,
>>
>> I have 2 groups (group 1 = 3 members, group 2 = 12 members) and I did
>> like to regress out the effects of groups + other variables by using doss.
>> However, whenever I specify doss with the mri_glmfit command, it gives me
>> an error message (see below). I saw that others have experienced similar
>> issues without any solutions. How can we solve this? Any insight is
>> appreciated.
>>
>> Best,
>> Paul
>>
>> mri_glmfit command:
>>
>> mri_glmfit --y
>> ../../freesurfer/subjects/tracula_output/stats/mcp.avg16_syn_bbr.FA.nii.gz
>> --fsgd dti_RPQ_3.fsgd doss --C dti_RPQ.mtx --o mcp_FA.glmdir --save-eres
>> --nii.gz
>>
>>
>> design.mtx:
>>
>> 0 0 0 0 0 0 0.5
>>
>>
>> Terminal output:
>>
>> gdfRead(): reading dti_RPQ_3.fsgd
>>
>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>>
>> Continuous Variable Means (all subjects)
>>
>> 0 Age 46.9333 9.86216
>>
>> 1 Sports 0.067 0.249444
>>
>> 2 Games 1.1 1.62754
>>
>> 3 Days_TBI 1903.2 907.81
>>
>> 4 RPQ_3 7 2.28035
>>
>> Class Size and Means of each Continuous Variable
>>
>> 1 PPCS_Male  3  33.   0.   2. 1337.3472   6.6667
>>
>> 2 PPCS_Female 12  50.   0.   0.8333 2044.6632   7.0833
>>
>> ERROR: Class PPCS_Male has 3 members. With 5 variables and using DODS,
>> you need at least 6 members
>>
>
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Re: [Freesurfer] mri_glmfit with doss isn't working. v7.2

[Douglas N. Greve]

Oh, I see what you mean. Can you try putting the line "DOSS" (no quotes) 
into your FSGD file?


On 1/3/2023 11:51 AM, miracle ozzoude wrote:


External Email - Use Caution

Hello Doug,

Thanks for the quick response. I did see the error. However, I 
specified doss in the mri_glmfit command and my mtx looks accurate as 
indicated above. Does that mean it can only work with dods? The reason 
I'm using 2 groups is because I want to regress out the effect of sex. 
However, the recommended way to do it in fsgd is to create a class for 
it and I only have 3 males.


Is there a workaround for this?

Many thanks.

On Fri, Dec 30, 2022 at 6:37 PM miracle ozzoude  
wrote:


Hello,

I have 2 groups (group 1 = 3 members, group 2 = 12 members) and I
did like to regress out the effects of groups + other variables by
using doss. However, whenever I specify doss with the mri_glmfit
command, it gives me an error message (see below). I saw that
others have experienced similar issues without any solutions. How
can we solve this? Any insight is appreciated.

Best,
Paul

mri_glmfit command:

mri_glmfit --y
../../freesurfer/subjects/tracula_output/stats/mcp.avg16_syn_bbr.FA.nii.gz
--fsgd dti_RPQ_3.fsgd doss --C dti_RPQ.mtx --o mcp_FA.glmdir
--save-eres --nii.gz


design.mtx:

0 0 0 0 0 0 0.5


Terminal output:

gdfRead(): reading dti_RPQ_3.fsgd

INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.

Continuous Variable Means (all subjects)

0 Age 46.9333 9.86216

1 Sports 0.067 0.249444

2 Games 1.1 1.62754

3 Days_TBI 1903.2 907.81

4 RPQ_3 7 2.28035

Class Size and Means of each Continuous Variable

1 PPCS_Male333. 0. 2. 1337.3472 6.6667

2 PPCS_Female 1250. 0. 0.8333 2044.6632 7.0833

ERROR: Class PPCS_Male has 3 members. With 5 variables and using
DODS, you need at least 6 members


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Re: [Freesurfer] mri_glmfit with doss isn't working. v7.2

[miracle ozzoude]

External Email - Use Caution

Hello Doug,

Thanks for the quick response. I did see the error. However, I specified
doss in the mri_glmfit command and my mtx looks accurate as indicated
above. Does that mean it can only work with dods? The reason I'm using 2
groups is because I want to regress out the effect of sex. However, the
recommended way to do it in fsgd is to create a class for it and I only
have 3 males.

Is there a workaround for this?

Many thanks.

On Fri, Dec 30, 2022 at 6:37 PM miracle ozzoude 
wrote:

> Hello,
>
> I have 2 groups (group 1 = 3 members, group 2 = 12 members) and I did like
> to regress out the effects of groups + other variables by using doss.
> However, whenever I specify doss with the mri_glmfit command, it gives me
> an error message (see below). I saw that others have experienced similar
> issues without any solutions. How can we solve this? Any insight is
> appreciated.
>
> Best,
> Paul
>
> mri_glmfit command:
>
> mri_glmfit --y
> ../../freesurfer/subjects/tracula_output/stats/mcp.avg16_syn_bbr.FA.nii.gz
> --fsgd dti_RPQ_3.fsgd doss --C dti_RPQ.mtx --o mcp_FA.glmdir --save-eres
> --nii.gz
>
>
> design.mtx:
>
> 0 0 0 0 0 0 0.5
>
>
> Terminal output:
>
> gdfRead(): reading dti_RPQ_3.fsgd
>
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>
> Continuous Variable Means (all subjects)
>
> 0 Age 46.9333 9.86216
>
> 1 Sports 0.067 0.249444
>
> 2 Games 1.1 1.62754
>
> 3 Days_TBI 1903.2 907.81
>
> 4 RPQ_3 7 2.28035
>
> Class Size and Means of each Continuous Variable
>
> 1 PPCS_Male  3  33.   0.   2. 1337.3472   6.6667
>
> 2 PPCS_Female 12  50.   0.   0.8333 2044.6632   7.0833
>
> ERROR: Class PPCS_Male has 3 members. With 5 variables and using DODS, you
> need at least 6 members
>
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Re: [Freesurfer] mri_glmfit with doss isn't working. v7.2

[Douglas N. Greve]

Is the error message not clear what the problem is?

On 12/30/2022 6:37 PM, miracle ozzoude wrote:


External Email - Use Caution

Hello,

I have 2 groups (group 1 = 3 members, group 2 = 12 members) and I did 
like to regress out the effects of groups + other variables by using 
doss. However, whenever I specify doss with the mri_glmfit command, it 
gives me an error message (see below). I saw that others have 
experienced similar issues without any solutions. How can we solve 
this? Any insight is appreciated.


Best,
Paul

mri_glmfit command:

mri_glmfit --y 
../../freesurfer/subjects/tracula_output/stats/mcp.avg16_syn_bbr.FA.nii.gz 
--fsgd dti_RPQ_3.fsgd doss --C dti_RPQ.mtx --o mcp_FA.glmdir 
--save-eres --nii.gz



design.mtx:

0 0 0 0 0 0 0.5


Terminal output:

gdfRead(): reading dti_RPQ_3.fsgd

INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.

Continuous Variable Means (all subjects)

0 Age 46.9333 9.86216

1 Sports 0.067 0.249444

2 Games 1.1 1.62754

3 Days_TBI 1903.2 907.81

4 RPQ_3 7 2.28035

Class Size and Means of each Continuous Variable

1 PPCS_Male333. 0. 2. 1337.3472 6.6667

2 PPCS_Female 1250. 0. 0.8333 2044.6632 7.0833

ERROR: Class PPCS_Male has 3 members. With 5 variables and using DODS, 
you need at least 6 members



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[Freesurfer] mri_glmfit with doss isn't working. v7.2

[miracle ozzoude]

External Email - Use Caution

Hello,

I have 2 groups (group 1 = 3 members, group 2 = 12 members) and I did like
to regress out the effects of groups + other variables by using doss.
However, whenever I specify doss with the mri_glmfit command, it gives me
an error message (see below). I saw that others have experienced similar
issues without any solutions. How can we solve this? Any insight is
appreciated.

Best,
Paul

mri_glmfit command:

mri_glmfit --y
../../freesurfer/subjects/tracula_output/stats/mcp.avg16_syn_bbr.FA.nii.gz
--fsgd dti_RPQ_3.fsgd doss --C dti_RPQ.mtx --o mcp_FA.glmdir --save-eres
--nii.gz


design.mtx:

0 0 0 0 0 0 0.5


Terminal output:

gdfRead(): reading dti_RPQ_3.fsgd

INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.

Continuous Variable Means (all subjects)

0 Age 46.9333 9.86216

1 Sports 0.067 0.249444

2 Games 1.1 1.62754

3 Days_TBI 1903.2 907.81

4 RPQ_3 7 2.28035

Class Size and Means of each Continuous Variable

1 PPCS_Male  3  33.   0.   2. 1337.3472   6.6667

2 PPCS_Female 12  50.   0.   0.8333 2044.6632   7.0833

ERROR: Class PPCS_Male has 3 members. With 5 variables and using DODS, you
need at least 6 members
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Re: [Freesurfer] mri_glmfit error

[Douglas N. Greve]

Do you see where it says "ERROR: READ THIS"? And below that do you see 
that it asks for four things? Can you send those four things?


On 10/5/2022 2:51 PM, fernanda rohrsetzer wrote:


External Email - Use Caution

Hi,
I attempted to execute mri_glmfit on my structural data through the following 
command - mri_glmfit --y lh.10.teste.thickness.mgh --fsgd testCT.fsgd --C 
Contrasts/LR-HR_testcov.mtx  --C Contrasts/LR-MDD_testcov.mtx --C 
Contrasts/HR-MDD_testcov.mtx --surf fsaverage lh --cortex --glmdir 
lh.groupteste.thickness.glmdir --eres-save

But it gives me an error (attached below) indicating a formatting problem in my 
FSGD file (attached).
I have been trying to figure that out for a while. But I am unable to debug it.
The design matrix (examining difference in thickness after controlling 
for effects of age, sex and Average thickness)


1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-HR_testcov.mtx

1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-MDD_testcov.mtx

0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > HR-MDD_testcov.mtx



Could someone please help me resolve it?
Thanks for your time.

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Re: [Freesurfer] mri_glmfit error

[fernanda rohrsetzer]

External Email - Use Caution

Ohh!!
I'm so sorry for my stupidity!!!
Thank you so much for your patience!!!



Em seg., 3 de out. de 2022 às 10:04, Douglas N. Greve <
dgr...@mgh.harvard.edu> escreveu:

> those are the contrast matrices. The design matrix will be in the output
> folder as file Xg.txt
>
> On 9/30/2022 11:43 AM, fernanda rohrsetzer wrote:
>
> External Email - Use Caution
> The design matrix (examining difference in thickness after controlling
> for effects of age, sex and Average thickness)
>
>
> 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-HR_testcov.mtx
>
>
> 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-MDD_testcov.mtx
>
>
> 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > HR-MDD_testcov.mtx
>
>
>
> Em sex., 30 de set. de 2022 às 13:35, Douglas N. Greve <
> dgr...@mgh.harvard.edu> escreveu:
>
>> almost there -- you did not include the 4th ittem
>>
>> On 9/30/2022 11:18 AM, fernanda rohrsetzer wrote:
>>
>> External Email - Use Caution
>> I'm so sorry...
>>
>> The FSGD file is attached (called "TestCT.txt).
>>
>> The design matrix (examining difference in thickness after controlling
>> for effects of age, sex and Average thickness)
>>
>>
>> 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-HR_testcov.mtx
>>
>>
>> 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-MDD_testcov.mtx
>>
>>
>> 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > HR-MDD_testcov.mtx
>>
>>
>> glmfit:
>>
>>
>> mri_glmfit --y lh.10.teste.volume.mgh --fsgd testCV.fsgd --C
>> Contrasts/LR-HR_testcov.mtx  --C Contrasts/LR-MDD_testcov.mtx --C
>> Contrasts/HR-MDD_testcov.mtx --surf fsaverage lh --cortex --glmdir
>> lh.groupteste.volume.glmdir --eres-save
>>
>>
>> Print of the screen is attached to (3 images).
>>
>> Thank you so much!!!
>> Fernanda
>>
>> Em sex., 30 de set. de 2022 às 11:25, Douglas N. Greve <
>> dgr...@mgh.harvard.edu> escreveu:
>>
>>> That terminal output asks you to send 4 things, but you only sent 2
>>>
>>> On 9/29/2022 11:51 AM, fernanda rohrsetzer wrote:
>>>
>>> External Email - Use Caution
>>>
>>> Hi,
>>> I attempted to execute  mri_glmfit on my structural data through the
>>> following command -
>>>
>>> mri_glmfit --y lh.10.teste.thickness.mgh --fsgd testCT.fsgd --C 
>>> Contrasts/LR-HR_testcov.mtx  --C Contrasts/LR-MDD_testcov.mtx --C 
>>> Contrasts/HR-MDD_testcov.mtx --surf fsaverage lh --cortex --glmdir 
>>> lh.groupteste.thickness.glmdir --eres-save
>>>
>>> But it gives me an error (attached below) indicating a formatting problem 
>>> in my FSGD file (attached).
>>> I have been trying to figure that out for a while. But I am unable to debug 
>>> it.
>>>
>>> Could someone please help me resolve it?
>>> Thanks for your time.
>>>
>>>
>>> ___
>>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
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>>> 
>>>
>>>
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Re: [Freesurfer] mri_glmfit error

[Douglas N. Greve]

those are the contrast matrices. The design matrix will be in the output 
folder as file Xg.txt


On 9/30/2022 11:43 AM, fernanda rohrsetzer wrote:


External Email - Use Caution

The design matrix (examining difference in thickness after controlling 
for effects of age, sex and Average thickness)



1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-HR_testcov.mtx


1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-MDD_testcov.mtx


0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > HR-MDD_testcov.mtx



Em sex., 30 de set. de 2022 às 13:35, Douglas N. Greve 
 escreveu:


almost there -- you did not include the 4th ittem

On 9/30/2022 11:18 AM, fernanda rohrsetzer wrote:


External Email - Use Caution

I'm so sorry...

The FSGD file is attached (called "TestCT.txt).

The design matrix (examining difference in thickness after
controlling for effects of age, sex and Average thickness)


1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-HR_testcov.mtx


1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-MDD_testcov.mtx


0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > HR-MDD_testcov.mtx


glmfit:


mri_glmfit --y lh.10.teste.volume.mgh --fsgd testCV.fsgd --C
Contrasts/LR-HR_testcov.mtx  --C Contrasts/LR-MDD_testcov.mtx --C
Contrasts/HR-MDD_testcov.mtx --surf fsaverage lh --cortex
--glmdir lh.groupteste.volume.glmdir --eres-save


Print of the screen is attached to (3 images).


Thank you so much!!!
Fernanda

Em sex., 30 de set. de 2022 às 11:25, Douglas N. Greve
 escreveu:

That terminal output asks you to send 4 things, but you only
sent 2

On 9/29/2022 11:51 AM, fernanda rohrsetzer wrote:


External Email - Use Caution

Hi,
I attempted to execute  mri_glmfit on my structural data through the
following command -

mri_glmfit --y lh.10.teste.thickness.mgh --fsgd testCT.fsgd --C 
Contrasts/LR-HR_testcov.mtx  --C Contrasts/LR-MDD_testcov.mtx --C 
Contrasts/HR-MDD_testcov.mtx --surf fsaverage lh --cortex --glmdir 
lh.groupteste.thickness.glmdir --eres-save

But it gives me an error (attached below) indicating a formatting 
problem in my FSGD file (attached).
I have been trying to figure that out for a while. But I am unable to 
debug it.

Could someone please help me resolve it?
Thanks for your time.

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Re: [Freesurfer] mri_glmfit error

[fernanda rohrsetzer]

External Email - Use Caution

The design matrix (examining difference in thickness after controlling for
effects of age, sex and Average thickness)


1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-HR_testcov.mtx


1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-MDD_testcov.mtx


0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > HR-MDD_testcov.mtx



Em sex., 30 de set. de 2022 às 13:35, Douglas N. Greve <
dgr...@mgh.harvard.edu> escreveu:

> almost there -- you did not include the 4th ittem
>
> On 9/30/2022 11:18 AM, fernanda rohrsetzer wrote:
>
> External Email - Use Caution
> I'm so sorry...
>
> The FSGD file is attached (called "TestCT.txt).
>
> The design matrix (examining difference in thickness after controlling
> for effects of age, sex and Average thickness)
>
>
> 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-HR_testcov.mtx
>
>
> 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-MDD_testcov.mtx
>
>
> 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > HR-MDD_testcov.mtx
>
>
> glmfit:
>
>
> mri_glmfit --y lh.10.teste.volume.mgh --fsgd testCV.fsgd --C
> Contrasts/LR-HR_testcov.mtx  --C Contrasts/LR-MDD_testcov.mtx --C
> Contrasts/HR-MDD_testcov.mtx --surf fsaverage lh --cortex --glmdir
> lh.groupteste.volume.glmdir --eres-save
>
>
> Print of the screen is attached to (3 images).
>
> Thank you so much!!!
> Fernanda
>
> Em sex., 30 de set. de 2022 às 11:25, Douglas N. Greve <
> dgr...@mgh.harvard.edu> escreveu:
>
>> That terminal output asks you to send 4 things, but you only sent 2
>>
>> On 9/29/2022 11:51 AM, fernanda rohrsetzer wrote:
>>
>> External Email - Use Caution
>>
>> Hi,
>> I attempted to execute  mri_glmfit on my structural data through the
>> following command -
>>
>> mri_glmfit --y lh.10.teste.thickness.mgh --fsgd testCT.fsgd --C 
>> Contrasts/LR-HR_testcov.mtx  --C Contrasts/LR-MDD_testcov.mtx --C 
>> Contrasts/HR-MDD_testcov.mtx --surf fsaverage lh --cortex --glmdir 
>> lh.groupteste.thickness.glmdir --eres-save
>>
>> But it gives me an error (attached below) indicating a formatting problem in 
>> my FSGD file (attached).
>> I have been trying to figure that out for a while. But I am unable to debug 
>> it.
>>
>> Could someone please help me resolve it?
>> Thanks for your time.
>>
>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>> be* 
>> https://secure-web.cisco.com/1QyCc3yzJVby05vR3KB830bnbrzsXoG9x_WaP4hE51gmUJMecn1__lKJlyoo9AtgJT9KQkPcLXt_iwWnsKx_mnj3fTIkN2ZNYrWuwZV_dg3kZm4G9f7nTzVkK4yYZRZCmKFRw0wVUpSEHrxH6HYFkEvjQVKb9BgbpgCCMFry31Qka3TmAKoH24TvBAOk9ZnHwv9Uhg55PfZto-90UgoWZjF_jeV0untKpPJG7EpH2dydWmOYZKUMEJAlnwEd1GlUQ6doeqjEwKdscjweEvuGmxHsrNMz_tqcnyEGGAML54ZRccLGF3UlaM27-P9m6-lOsDcxkuhAQVx7yv981mODONw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>  
>> 
>>
>>
>> ___
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>> 
>> The information in this e-mail is intended only for the person to whom it
>> is addressed.  If you believe this e-mail was sent to you in error and the
>> e-mail contains patient information, please contact the Mass General
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Re: [Freesurfer] mri_glmfit error

[Douglas N. Greve]

almost there -- you did not include the 4th ittem

On 9/30/2022 11:18 AM, fernanda rohrsetzer wrote:


External Email - Use Caution

I'm so sorry...

The FSGD file is attached (called "TestCT.txt).

The design matrix (examining difference in thickness after controlling 
for effects of age, sex and Average thickness)



1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-HR_testcov.mtx


1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > LR-MDD_testcov.mtx


0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 > HR-MDD_testcov.mtx


glmfit:


mri_glmfit --y lh.10.teste.volume.mgh --fsgd testCV.fsgd --C 
Contrasts/LR-HR_testcov.mtx  --C Contrasts/LR-MDD_testcov.mtx --C 
Contrasts/HR-MDD_testcov.mtx --surf fsaverage lh --cortex --glmdir 
lh.groupteste.volume.glmdir --eres-save



Print of the screen is attached to (3 images).


Thank you so much!!!
Fernanda

Em sex., 30 de set. de 2022 às 11:25, Douglas N. Greve 
 escreveu:


That terminal output asks you to send 4 things, but you only sent 2

On 9/29/2022 11:51 AM, fernanda rohrsetzer wrote:


External Email - Use Caution

Hi,
I attempted to execute  mri_glmfit on my structural data through the
following command -

mri_glmfit --y lh.10.teste.thickness.mgh --fsgd testCT.fsgd --C 
Contrasts/LR-HR_testcov.mtx  --C Contrasts/LR-MDD_testcov.mtx --C 
Contrasts/HR-MDD_testcov.mtx --surf fsaverage lh --cortex --glmdir 
lh.groupteste.thickness.glmdir --eres-save

But it gives me an error (attached below) indicating a formatting problem 
in my FSGD file (attached).
I have been trying to figure that out for a while. But I am unable to debug 
it.

Could someone please help me resolve it?
Thanks for your time.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
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>
.


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The information in this e-mail is int

Re: [Freesurfer] mri_glmfit error

[Douglas N. Greve]

That terminal output asks you to send 4 things, but you only sent 2

On 9/29/2022 11:51 AM, fernanda rohrsetzer wrote:


External Email - Use Caution

Hi,
I attempted to execute  mri_glmfit on my structural data through the
following command -

mri_glmfit --y lh.10.teste.thickness.mgh --fsgd testCT.fsgd --C 
Contrasts/LR-HR_testcov.mtx  --C Contrasts/LR-MDD_testcov.mtx --C 
Contrasts/HR-MDD_testcov.mtx --surf fsaverage lh --cortex --glmdir 
lh.groupteste.thickness.glmdir --eres-save

But it gives me an error (attached below) indicating a formatting problem in my 
FSGD file (attached).
I have been trying to figure that out for a while. But I am unable to debug it.

Could someone please help me resolve it?
Thanks for your time.

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] mri_glmfit error

[fernanda rohrsetzer]

External Email - Use Caution

Hi,
I attempted to execute  mri_glmfit on my structural data through the
following command -

mri_glmfit --y lh.10.teste.thickness.mgh --fsgd testCT.fsgd --C
Contrasts/LR-HR_testcov.mtx  --C Contrasts/LR-MDD_testcov.mtx --C
Contrasts/HR-MDD_testcov.mtx --surf fsaverage lh --cortex --glmdir
lh.groupteste.thickness.glmdir --eres-save

But it gives me an error (attached below) indicating a formatting
problem in my FSGD file (attached).
I have been trying to figure that out for a while. But I am unable to debug it.

Could someone please help me resolve it?
Thanks for your time.
GroupDescriptorFile 1   
Title W0
Class LRmale
Class LRfemale  
Class HRmale
Class HRfemale  
Class MDDmale   
Class MDDfemale 
Variable age AverageThickmm 

Input   sub0109306  MDDfemale   14.52.623745
Input   sub0209110  HRfemale14.12.578705
Input   sub0211107  MDDfemale   16.42.57688
Input   sub0310211  LRmale  15.52.678785
Input   sub0310411  MDDfemale   16.12.66405
Input   sub0310703  MDDfemale   15.32.499575
Input   sub0310706  HRfemale16.12.59593
Input   sub0310710  MDDfemale   15.42.721905
Input   sub0311303  MDDfemale   15.92.573815
Input   sub0311313  HRfemale16.62.542145
Input   sub0320307  HRmale  16.62.585265
Input   sub0408108  HRmale  15.12.619365
Input   sub0410108  MDDfemale   16.62.57616
Input   sub0508205  HRmale  14.42.51086
Input   sub0509113  MDDfemale   15.42.578945
Input   sub0509207  MDDfemale   16.32.544425
Input   sub0611106  MDDmale 16.82.60941
Input   sub0612205  MDDfemale   16.82.612995
Input   sub0612304  MDDmale 16.92.49735
Input   sub0708204  LRmale  14.12.53706
Input   sub0709122  LRfemale15.12.707045
Input   sub0709123  MDDmale 15.52.63077
Input   sub0709213  LRfemale14.72.579635
Input   sub0808209  LRmale  14.32.67927
Input   sub0921204  LRfemale15.82.742015
Input   sub1009113  HRfemale15.22.546395
Input   sub1009211  MDDfemale   15.52.48501
Input   sub1009302  MDDfemale   17.02.603955
Input   sub1010203  MDDfemale   16.42.59446
Input   sub1020401  MDDfemale   16.22.547875
Input   sub1308106  MDDfemale   15.72.656165
Input   sub1309216  MDDmale 16.02.622425
Input   sub1310506  HRmale  16.92.55924
Input   sub1408101  HRmale  15.22.69717
Input   sub1510114  MDDfemale   16.42.62951
Input   sub1709105  MDDfemale   15.52.56878
Input   sub1709111  MDDfemale   14.82.57653
Input   sub1709113  MDDfemale   15.72.63139
Input   sub1810103  HRmale  16.62.529805
Input   sub1810208  MDDfemale   15.42.59504
Input   sub1820403  MDDfemale   16.82.587325
Input   sub2110309  HRmale  16.62.55233
Input   sub2110704  HRmale  16.62.542835
Input   sub2120305  LRfemale16.92.715215
Input   sub2208106  HRmale  15.62.56209
Input   sub2308201  LRmale  14.52.750915
Input   sub2308209  HRmale  15.32.60082
Input   sub2309206  MDDmale 15.42.64781
Input   sub2309208  LRmale  14.82.6226
Input   sub2408101  MDDmale 14.92.584215
Input   sub2408207  LRfemale14.02.754575
Input   sub2610104  HRmale  16.22.73419
Input   sub2610117  LRmale  16.22.64692
Input   sub2908106  MDDmale 14.12.624275
Input   sub2908203  HRfemale15.42.660925
Input   sub3020206  HRmale  16.92.556665
Input   sub3110310  MDDmale 16.72.642625
Input   sub3111412  HRmale  16.02.592335
Input   sub3120303  MDDmale 16.52.52596
Input   sub3120314  MDDmale 16.82.571405
Input   sub3120404  LRmale  16.32.585195
Input   sub3408210  LRfemale14.62.55676
Input   sub3409113  LRfemale14.62.386085
Input   sub3508203  HRfemale16.82.64059
Input   sub3608104  HRmale  16.82.58839
Input   sub3809205  LRfemale15.32.724225
Input   sub3909013  LRfemale15.52.665965
Input   sub4210201  MDDmale   

Re: [Freesurfer] mri_glmfit error: MatrixResidualForming(): X is not invertable

[Piot, Alex]

External Email - Use Caution

Thanks so much, Doug that worked!


--

Alexandre Piot
Clinical Neuroscience MSc. -- Queen Square Institute of Neurology
President of the Application of Psychedelics Society 
<https://secure-web.cisco.com/14QCtn-rMuCXkiml5_4I5IXFKX66Ncu_AGQ8fvExAsL8gWmxqQcHvd2kGWlDCWvSUOfbLDIjXuX3fuQKO-5eyxhZtT30_7hevE8ltwjNXtghqCjtxi2goS8fo38AME_JY9Fqvuif0tSqY4AZuGkRPYPkLdalnLLMU_q3HNsXjk5z6GClTBOx70-LsoFWh--kA6Y3E1Em-ctQJMV9H_D6MbP6NLDJh03ORTTAVtQxMFxpN1GKFRQ6syUz1sOwHXX7d5Bj9mJeTbtKUuCJCER7oBDA_w6czmo1uikYUgjiqoTmcrevVlIcDiHMZEKkfvqxE/https%3A%2F%2Fwww.uclsap.com%2F>
 -- UCL
UNITy 
Project<https://secure-web.cisco.com/1NtBKC7uL_DuYiDb5y-hj20dZDvYr9ijFl1uMQerXX8XxG6cgyVrXGkykk6AzP-78-d8I12EmGuFwqaRB-JakskN_fsg1PtgtbsB6D7xicxnvYXom36ocXwx1hCTyBPioBd66_J-C7FFSSrIxlSpytGrr7PBQXtBGl9FkNuiTgGrFFgiBeX9LGov1zV6MVOrR3M2jSPnd5u-d13ucPwNneHlLWVfMtQdOnutlBO_1tkJ3G23_Hg_cICSTgxSN0wWJkuT-RxhGjxlnzwcr2vM2cEeoy_ubgepgY09Dg8whkWQDwyvc2fpfyUWH2kVZjDEk/https%3A%2F%2Fwww.psychedelicunit.com%2F>



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Wednesday, September 7, 2022 3:50 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mri_glmfit error: MatrixResidualForming(): X is not 
invertable


⚠ Caution: External sender

My guess is that the variable (G_cingul vol) should be normalized (remove the 
mean and divide by the stddev).

On 9/6/2022 5:44 PM, Piot, Alex wrote:

External Email - Use Caution

Hello Freesurfer experts,

I am trying to perform a GLM, using the volume of a brain region as a 
covariate. I am doing a two-group, one covariate design. I originally tried to 
use QDEC to facilitate the process and received an error message that the 
mri_glmfit command had failed. I then saw that QDEC was deprecated and followed 
the instructions set out on the freesurfer wiki for doing it manually 
(MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1AVbn8ayTwZ1pIMwfAGmvXnOUKpv-ZxIzALR0W6MmXrotHqLKC8xftaolrrP8EOGYzkcEN-XSXAzUBiUIcrb3cmlXt02aROvfz926ghj0MWyRQPl35sAgCznxlcyg2jhiaPSIRxxZpp5aFvsVkjYsYtchwmKUxlwCoRoKBViKQkBTj1y8ywaaUmHGsBeA_hikaeB22gS4LFTDpc0xJEG8FuxgJUjyKFv4e9Ti-asXg9k2zIN5S_33Piw5odUY4j_wlzL92nasF4YatJhV07knf47BDzE8lkGNd_qWsLrlO_HBIv7uMSM0yPgITWUj5vND4fFVeSqPq4HcMXmWJ2lSog/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0<https://secure-web.cisco.com/1L6dm2yjf87UmfZNslR1O80hp2NRnPaRHt2XfHNiM9VKLumGdZWe18tsgJY8NM4r2MF8Ab3UK0ehExtk3fp4BlaA4mUnGZ8HkHXv_n1swN689JVdxqODicn5lWi-KNJKXxB2aj7Uv4nz3rlbRHc040ZmE3BGrEGUnjPna0nWEd6vqpl-P85nWzaKRkVDp3Xo4jKJeTeCgPcHODDlSokdIXAx68bHm1VZoRZLlR9cOFtwsHBTlw8YvSGuuTl2o1M-X1c9lwhTWMQIL0Omc7ePvtQgHWIiZlga_IUB3SBZYeIPe41s38UiXHUTomPdG0uiU1ZsltbSFnbs2DflkU01YtQ/https%3A%2F%2Feur01.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1W0gEAYXZeH6XMYzikihrf4Ct-vcV_3e-WmTr1eqTVlVGWz8ZAzr0ToHAdQVWw6seyPj2yu31w7pqzGFZrFu7wQ5so3ZFfYQjKCTQ_ExMc1qL3caPs38GvVhvpKQ2NXDmLYaNxgZkGAilAmdd8JnWqAEkh_EBy23scDzimQ4p5fuMO002JYf6Si2hgy5xDHl5Yf748DEHIe1u3vA-E3BtAxiCGBB67Hm4Dc6xHuUk_Na_DLM_uYMDcy3z8UttfwM1TTMP0_JLn_rmvpcqSqGN2rtaA3UGOE5aOOm0GnQgDXQWm5MIgG9_A0PeUuBfAxRgunRr7ZxcVBapNEIOwCUPdg%252Fhttps%25253A%25252F%25252Fsurfer.nmr.mgh.harvard.edu%25252Ffswiki%25252FFsTutorial%25252FGroupAnalysisV6.0%26data%3D05%257C01%257Calexandre.piot.20%2540ucl.ac.uk%257C73c035e9e6cf487d2e5108da907c2a21%257C1faf88fea9984c5b93c9210a11d9a5c2%257C0%257C0%257C63798116035295%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%257C%257C%257C%26sdata%3DLh6n24JxgAem7SrBwdAYGJdgM594SN2DrIfBZNPVDSc%253D%26reserved%3D0>).

I received the same error message as I had with QDEC on the command line:

ERROR: MatrixResidualForming(): X is not invertable
RD is not invertable n = 1

This only occurs for certain of the brain regions used as covariates; for 
others, the QDEC and command-line streams work perfectly. Additionally, I've 
noticed that if I input different numbers for the covariate values in the fsgd 
file, the command runs smoothly.

I haven't been able to find a similar error on the mailing list, does anyone 
have an idea of how to work around this? I would greatly appreciate it.

Please find attached my fsgd file, and the full log of what happens after I run 
the mri_glmfit command (when it works and when it doesn't)
The hands.fsgd file doesn't work, whereas the hands_works.fsgd file does.

Freesurfer version: 7.2.0, Ubuntu 20.04, Windows WSL

Best wishes,
Alex

--

Alexandre Piot, MSc.
Queen Square Institute of Neurology
President of the Application of Psy

Re: [Freesurfer] mri_glmfit error: MatrixResidualForming(): X is not invertable

[Douglas N. Greve]

My guess is that the variable (G_cingul vol) should be normalized 
(remove the mean and divide by the stddev).


On 9/6/2022 5:44 PM, Piot, Alex wrote:


External Email - Use Caution

Hello Freesurfer experts,

I am trying to perform a GLM, using the volume of a brain region as a 
covariate. I am doing a two-group, one covariate design. I originally 
tried to use QDEC to facilitate the process and received an error 
message that the mri_glmfit command had failed. I then saw that QDEC 
was deprecated and followed the instructions set out on the freesurfer 
wiki for doing it manually (*MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0 
). 



I received the same error message as I had with QDEC on the command line:

ERROR: MatrixResidualForming(): X is not invertable
RD is not invertable n = 1

This only occurs for certain of the brain regions used as covariates; 
for others, the QDEC and command-line streams work perfectly. 
Additionally, I've noticed that if I input different numbers for the 
covariate values in the fsgd file, the command runs smoothly.


I haven't been able to find a similar error on the mailing list, does 
anyone have an idea of how to work around this? I would greatly 
appreciate it.


Please find attached my fsgd file, and the full log of what happens 
after I run the mri_glmfit command (when it works and when it doesn't)

The hands.fsgd file doesn't work, whereas the hands_works.fsgd file does.

Freesurfer version: 7.2.0, Ubuntu 20.04, Windows WSL

Best wishes,
Alex

--

Alexandre Piot, MSc.
Queen Square Institute of Neurology
President of the Application of Psychedelics Society 
-- 
UCL
UNITy Project 





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[Freesurfer] mri_glmfit error: MatrixResidualForming(): X is not invertable

[Piot, Alex]

External Email - Use Caution

Hello Freesurfer experts,

I am trying to perform a GLM, using the volume of a brain region as a 
covariate. I am doing a two-group, one covariate design. I originally tried to 
use QDEC to facilitate the process and received an error message that the 
mri_glmfit command had failed. I then saw that QDEC was deprecated and followed 
the instructions set out on the freesurfer wiki for doing it manually 
(https://secure-web.cisco.com/1W0gEAYXZeH6XMYzikihrf4Ct-vcV_3e-WmTr1eqTVlVGWz8ZAzr0ToHAdQVWw6seyPj2yu31w7pqzGFZrFu7wQ5so3ZFfYQjKCTQ_ExMc1qL3caPs38GvVhvpKQ2NXDmLYaNxgZkGAilAmdd8JnWqAEkh_EBy23scDzimQ4p5fuMO002JYf6Si2hgy5xDHl5Yf748DEHIe1u3vA-E3BtAxiCGBB67Hm4Dc6xHuUk_Na_DLM_uYMDcy3z8UttfwM1TTMP0_JLn_rmvpcqSqGN2rtaA3UGOE5aOOm0GnQgDXQWm5MIgG9_A0PeUuBfAxRgunRr7ZxcVBapNEIOwCUPdg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0).

I received the same error message as I had with QDEC on the command line:

ERROR: MatrixResidualForming(): X is not invertable
RD is not invertable n = 1

This only occurs for certain of the brain regions used as covariates; for 
others, the QDEC and command-line streams work perfectly. Additionally, I've 
noticed that if I input different numbers for the covariate values in the fsgd 
file, the command runs smoothly.

I haven't been able to find a similar error on the mailing list, does anyone 
have an idea of how to work around this? I would greatly appreciate it.

Please find attached my fsgd file, and the full log of what happens after I run 
the mri_glmfit command (when it works and when it doesn't)
The hands.fsgd file doesn't work, whereas the hands_works.fsgd file does.

Freesurfer version: 7.2.0, Ubuntu 20.04, Windows WSL

Best wishes,
Alex

--

Alexandre Piot, MSc.
Queen Square Institute of Neurology
President of the Application of Psychedelics Society 

 -- UCL
UNITy 
Project




mri_glmfit.log
Description: mri_glmfit.log


hand.fsgd
Description: hand.fsgd
mri_glmfit --y 
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/y.mgh
 
--fsgd 
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/hands_works.fsgd
 
--glmdir 
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi
 
--surf fsaverage lh --label 
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/fsaverage/label/lh.aparc.label
 
--C 
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Avg-Intercept-volume.mat
 
--C 
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Avg-volume-lh_cingul-ant_volume-Cor.mat
 
--C 
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Diff-Ayahuasca-Control-Intercept-volume.mat
 
--C 
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/contrasts/lh-Diff-Ayahuasca-Control-Cor-volume-lh_cingul-ant_volume.mat
  

gdfRead(): reading 
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/hands_works.fsgd
 
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. 
Continuous Variable Means (all subjects) 
0 lh_G_frontomargin_volume 2404.2 361.981
Class Size and Means of each Continuous Variable
1 GroupAyahuasca 22 2355.0909
2 GroupControl 22 2453.3182 
INFO: gd2mtx_method is dods 
Reading source surface 
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 65417.00 
AvgVtxArea   0.399269
AvgVtxDist   0.721953 
StdVtxDist   0.195472  
 7.2.0 
cwd 
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi
 
cmdline mri_glmfit --y 
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/y.mgh
 --fsgd 
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi/hands_works.fsgd
 --glmdir 
/usr/local/freesurfer/7.2.0/subjects/Ayahuasca_Data_paired/qdec/Leftantcingut_LeftHemi
 --surf fsaverage lh --labe

Re: [Freesurfer] mri_glmfit error

[Douglas N. Greve]

You don't have enough members in the classes to fit the model that you 
have. Eg, class d has 4 members with which you are fitting an offset and 
3 slopes leaving you with 0 degrees of freedom. You need to get more 
subjects or change your model. btw, gender is usually modeled as a 
discrete rather than continuous covariate.


On 4/11/2022 8:06 AM, David wrote:


External Email - Use Caution

Hello FreeSurfer Developers,
my fsgd is this：
GroupDescriptorFile 1
Title post compane
Class d
Class m
Class h

RescaleFlag 1
DemeanFlag 1
Variables gender Age Edu
Input bd1 d 0 15 8
Input bd2 d 1 19 13
Input bd7 d 0 17 11
Input bd8 d 1 19 13
Input bd6 m 1 22 12
Input bd9 m 1 26 7
Input bd10 m 0 53 15
Input bd11 m 1 56 4
Input hc3 h 0 45 7
Input hc4 h 1 18 13
Input hc1 h 0 52 7
Input hc2 h 1 24 10

When I run Three Groups (One Factor/Three Levels), three Covariates,my 
MTX is


1 -1 0 0 0 0 0 0 0 0 0 0
1 0 -1 0 0 0 0 0 0 0 0 0
It’s wrong,What should I do

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08



 ERROR: READ THIS -
--vv-
Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
    mri_glmfit --y rh_teach66.mgh --fsgd glmteach66.fsgd --C 
glmteach66.mtx --glmdir group66.area_66sm.rh --fwhm 10 --surface 
fsaverage rh --eres-save
  2. The terminal output of this program (ie, everything it prints to 
the screen)

  3. The FSGD file (glmteach66.fsgd)
  4. The design matrix group66.area_66sm.rh/Xg.dat
Attempting to diagnose further
WARNING: Class d has 4 members. With 3 variables and using DODS, This 
is the bare minimum which may cause problems with the design matrix.
WARNING: Class m has 4 members. With 3 variables and using DODS, This 
is the bare minimum which may cause problems with the design matrix.
WARNING: Class h has 4 members. With 3 variables and using DODS, This 
is the bare minimum which may cause problems with the design matrix.

SumSq: Min=1.491914 (col 10), Max=2.676059 (col 11)
 ... could not determine the cause of the problem
--


ERROR: cannot find residual group66.area_66sm.lh/eres needed with 
--perm-resid

  when running mri_glmfit, make sure to include --eres-save
ERROR: cannot find residual group66.area_66sm.rh/eres needed with 
--perm-resid

  when running mri_glmfit, make sure to include --eres-save
glm66.sh: line 14: --perm-resid: command not found
---





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The information in this e-mail is intended only for the person to whom it is 
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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] mri_glmfit error

[David]

External Email - Use Caution

Hello FreeSurfer Developers,
my fsgd is this：
GroupDescriptorFile 1
Title post compane
Class d
Class m
Class h

RescaleFlag 1
DemeanFlag 1
Variables gender Age Edu
Input bd1 d 0 15 8
Input bd2 d 1 19 13
Input bd7 d 0 17 11
Input bd8 d 1 19 13
Input bd6 m 1 22 12
Input bd9 m 1 26 7
Input bd10 m 0 53 15
Input bd11 m 1 56 4
Input hc3 h 0 45 7
Input hc4 h 1 18 13
Input hc1 h 0 52 7
Input hc2 h 1 24 10


When I run Three Groups (One Factor/Three Levels), three Covariates,my MTX is

1 -1 0 0 0 0 0 0 0 0 0 0
1 0 -1 0 0 0 0 0 0 0 0 0
It’s wrong,What should I do

ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08



 ERROR: READ THIS -
--vv-
Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit --y rh_teach66.mgh --fsgd glmteach66.fsgd --C glmteach66.mtx 
--glmdir group66.area_66sm.rh --fwhm 10 --surface fsaverage rh --eres-save
  2. The terminal output of this program (ie, everything it prints to the 
screen)
  3. The FSGD file (glmteach66.fsgd)
  4. The design matrix group66.area_66sm.rh/Xg.dat
Attempting to diagnose further
WARNING: Class d has 4 members. With 3 variables and using DODS, This is the 
bare minimum which may cause problems with the design matrix.
WARNING: Class m has 4 members. With 3 variables and using DODS, This is the 
bare minimum which may cause problems with the design matrix.
WARNING: Class h has 4 members. With 3 variables and using DODS, This is the 
bare minimum which may cause problems with the design matrix.
SumSq: Min=1.491914 (col 10), Max=2.676059 (col 11)
 ... could not determine the cause of the problem
--


ERROR: cannot find residual group66.area_66sm.lh/eres needed with --perm-resid
  when running mri_glmfit, make sure to include --eres-save
ERROR: cannot find residual group66.area_66sm.rh/eres needed with --perm-resid
  when running mri_glmfit, make sure to include --eres-save
glm66.sh: line 14: --perm-resid: command not found
---
___
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Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

[정현우]

External Email - Use Caution

Hi Dr. Greve,

Thank you very much for your solution. That solved the problem.

I genuinely appreciate your support!

Best,
Hyunwoo Jeong

2022년 3월 10일 (목) 오전 2:52, Douglas N. Greve 님이 작성:

> The problem is that your design matrix is badly scaled. The eTIV values
> are much larger than the group membership (value=1). Try subtracting the
> mean of the eTIV and dividing by the stddev to normalize it.
>
>
> On 2/25/2022 8:07 PM, 정현우 wrote:
>
> External Email - Use Caution
> Hi Dr. Greve,
>
> Thank you for your response. I uploaded the .mgh, .fsgd, and .mtx files
> that I used to run the mri_glmfit command. I can upload the recon-all
> outputs of the individual samples as well, if needed. The files are
> uploaded in google drive, please access them via the link below.
>
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1OSqR9RniGPyWuFMchLKO678Wi2STTGhXTdrWB93Dvxpp0D8X0W8OLeVfExQQz7p0kQqayDn3ySQxM9CxrtY8igbR9kqzlm7l90460XSu1uKZC4NzDn_HBkQQ1NPMMyb1RuV_1vYGs_m3H7VdUayjO88cs1-DTC8eAnsE8WsPcGfMw-CevWVhDu3mlbBBooXuPA01rU6yPLXYtR32L3KgIZF3UHHOl0Os4dsciWtU0mlHS4Tuvy4KzqrpbRbB19sXGcDUgtjIfpDfZMgROJjI5_4eDgKgTQtDtcI3_7jweaVpaEt915oj4PQ0N-kaSm4D/https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F1QNzMxJdmc7Bo1KGlh9OC9f7DVzZ9ej2k%3Fusp%3Dsharing
> 
>
> Thank you in advance,
> Hyunwoo Jeong.
>
>
>
> 2022년 2월 26일 (토) 오전 8:16, Douglas N. Greve 님이 작성:
>
>> Can you upload the data to me somewhere? I'd need the input volume and
>> the fsgd and any contrasts
>>
>> On 2/21/2022 10:24 PM, 정현우 wrote:
>>
>> External Email - Use Caution
>> Hi Dr. Greve,
>>
>> Thank you for your suggestion. Unfortunately, the same problem occurred
>> when I ran the command with --no-pcc. Folders and files with the same names
>> were created. and the following error message (identical to the previous
>> one) appeared.
>>
>> error: No such file or directory
>> error: MatrixMultiplyD(): m2 is null
>>  break
>> /home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596
>>
>> Do you have any other suggestions? I appreciate your help so far.
>>
>> Best,
>> Hyunwoo Jeong
>>
>> 2022년 2월 17일 (목) 오전 10:18, 정현우 님이 작성:
>>
>>> Hi Dr. Greve,
>>>
>>> Thank you for your suggestion. Unfortunately, the same problem occurred
>>> when I ran the command with --no-pcc. Folders and files with the same names
>>> were created. and the following error message (identical to the previous
>>> one) appeared.
>>>
>>> error: No such file or directory
>>> error: MatrixMultiplyD(): m2 is null
>>>  break
>>> /home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596
>>>
>>> Do you have any other suggestions? I appreciate your help so far.
>>>
>>> Best,
>>> Hyunwoo Jeong
>>>
>>> 2022년 2월 17일 (목) 오전 1:41, Douglas N. Greve 님이
>>> 작성:
>>>
 It looks like it is failing when computing the partial correlation
 coef. Try  running it with --no-pcc

 On 2/16/2022 10:53 AM, 정현우 wrote:

 External Email - Use Caution
 Hi Dr. Greve,

 Yes, it seems like the output folder and some output files were created.

 After running the mri_glmfit, 'three_group_comparison.area.lh.glmdir'
 folder was created. In the glmdir folder, 'three_group_comparison.area'
 folder was created, and the following files were also created: beta.mgh,
 dof.dat, eres.mgh, fwhm.dat, mask.mgh, mri_glmfit.log, rstd.mgh, rvar.mgh,
 sar1.mgh, surface, and Xg.dat.

 In the 'three_group_comparison.area' folder, the following files were
 created: C.dat, F.mgh, gamma.mgh, maxvox.dat, sig.mgh, and z.mgh.

 Do you have any idea what could have been the problem?

 Thanks,
 Hyunwoo Jeong

 2022년 2월 17일 (목) 오전 12:36, Douglas N. Greve 님이
 작성:

> Did it create the output folder and some output files? I noticed that
> there is a "error: No such file or directory" error 
>
> On 2/14/2022 8:46 PM, 정현우 wrote:
>
> External Email - Use Caution
> Hi Dr. Greve,
>
> Thank you for your reply. I attached the fsgd file, mtx file and the
> Xg.dat file below.
>
> Hyunwoo Jeong
>
> 2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve 님이
> 작성:
>
>> can you send your fsgd file and the Xg.dat file?
>>
>> On 2/14/2022 1:21 AM, 정현우 wrote:
>>
>> External Email - Use Caution
>> Hello FreeSurfe

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

[Douglas N. Greve]

The problem is that your design matrix is badly scaled. The eTIV values 
are much larger than the group membership (value=1). Try subtracting the 
mean of the eTIV and dividing by the stddev to normalize it.



On 2/25/2022 8:07 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Thank you for your response. I uploaded the .mgh, .fsgd, and .mtx 
files that I used to run the mri_glmfit command. I can upload 
the recon-all outputs of the individual samples as well, if needed. 
The files are uploaded in google drive, please access them via the 
link below.


*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://drive.google.com/drive/folders/1QNzMxJdmc7Bo1KGlh9OC9f7DVzZ9ej2k?usp=sharing 



Thank you in advance,
Hyunwoo Jeong.



2022년 2월 26일 (토) 오전 8:16, Douglas N. Greve 
님이 작성:


Can you upload the data to me somewhere? I'd need the input volume
and the fsgd and any contrasts

On 2/21/2022 10:24 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Thank you for your suggestion. Unfortunately, the same problem
occurred when I ran the command with --no-pcc. Folders and files
with the same names were created. and the following error message
(identical to the previous one) appeared.

error: No such file or directory
error: MatrixMultiplyD(): m2 is null
 break

/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596

Do you have any other suggestions? I appreciate your help so far.

Best,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 10:18, 정현우 님이
작성:

Hi Dr. Greve,

Thank you for your suggestion. Unfortunately, the same
problem occurred when I ran the command with --no-pcc.
Folders and files with the same names were created. and the
following error message (identical to the previous one) appeared.

error: No such file or directory
error: MatrixMultiplyD(): m2 is null
 break

/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596

Do you have any other suggestions? I appreciate your help so far.

Best,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 1:41, Douglas N. Greve
님이 작성:

It looks like it is failing when computing the partial
correlation coef. Try  running it with --no-pcc

On 2/16/2022 10:53 AM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Yes, it seems like the output folder and some output
files were created.

After running the mri_glmfit,
'three_group_comparison.area.lh.glmdir' folder was
created. In the glmdir folder,
'three_group_comparison.area' folder was created, and
the following files were also created: beta.mgh,
dof.dat, eres.mgh, fwhm.dat, mask.mgh, mri_glmfit.log,
rstd.mgh, rvar.mgh, sar1.mgh, surface, and Xg.dat.

In the 'three_group_comparison.area' folder, the
following files were created: C.dat, F.mgh, gamma.mgh,
maxvox.dat, sig.mgh, and z.mgh.

Do you have any idea what could have been the problem?

Thanks,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 12:36, Douglas N. Greve
님이 작성:

Did it create the output folder and some output
files? I noticed that there is a "error: No such
file or directory" error 

On 2/14/2022 8:46 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Thank you for your reply. I attached the fsgd file,
mtx file and the Xg.dat file below.

Hyunwoo Jeong

2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve
님이 작성:

can you send your fsgd file and the Xg.dat file?

On 2/14/2022 1:21 AM, 정현우 wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to compare cortical surface
area among three groups while controlling for
estimated total intracranial volume (eTIV), as
described on the Surface Based Group Analysis
tutorial (*MailSc

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

[정현우]

External Email - Use Caution

Hi Dr. Greve,

Thank you for your response. I uploaded the .mgh, .fsgd, and .mtx files
that I used to run the mri_glmfit command. I can upload the recon-all
outputs of the individual samples as well, if needed. The files are
uploaded in google drive, please access them via the link below.

https://secure-web.cisco.com/1dyd7-xjzX4Lq_6TpVFINCBx2OzGb31QOy2b8WE4RlFK-rQW7JTWTbadgXYRKAnzQhyfbYr9ZYTmLKlwKzSSQ4tMlXDsMkhJgQ181lHtFxzXgb_Dry1feAP8aKFqOXA1x-F4FuNAsaU8BolN83rf62nnKC8adsct_OhZVZYRMXe1RciKtM0FCMjooYYAmkUm3qRc7PDz8BtLyoRaBXtfZE5nsVlYanmwZSr2cbx0n4upHQjEdEUkJRoX-4GMRt5qLHTNxfJ1mrN8SJ3vMTeBuBdNo8CCqaFKBm3Lb0rAycL-Ir-ihasFHFqKxRhpfCxVCNtXsrjGigkWr7ym9LaK0nw/https%3A%2F%2Fdrive.google.com%2Fdrive%2Ffolders%2F1QNzMxJdmc7Bo1KGlh9OC9f7DVzZ9ej2k%3Fusp%3Dsharing

Thank you in advance,
Hyunwoo Jeong.



2022년 2월 26일 (토) 오전 8:16, Douglas N. Greve 님이 작성:

> Can you upload the data to me somewhere? I'd need the input volume and the
> fsgd and any contrasts
>
> On 2/21/2022 10:24 PM, 정현우 wrote:
>
> External Email - Use Caution
> Hi Dr. Greve,
>
> Thank you for your suggestion. Unfortunately, the same problem occurred
> when I ran the command with --no-pcc. Folders and files with the same names
> were created. and the following error message (identical to the previous
> one) appeared.
>
> error: No such file or directory
> error: MatrixMultiplyD(): m2 is null
>  break
> /home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596
>
> Do you have any other suggestions? I appreciate your help so far.
>
> Best,
> Hyunwoo Jeong
>
> 2022년 2월 17일 (목) 오전 10:18, 정현우 님이 작성:
>
>> Hi Dr. Greve,
>>
>> Thank you for your suggestion. Unfortunately, the same problem occurred
>> when I ran the command with --no-pcc. Folders and files with the same names
>> were created. and the following error message (identical to the previous
>> one) appeared.
>>
>> error: No such file or directory
>> error: MatrixMultiplyD(): m2 is null
>>  break
>> /home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596
>>
>> Do you have any other suggestions? I appreciate your help so far.
>>
>> Best,
>> Hyunwoo Jeong
>>
>> 2022년 2월 17일 (목) 오전 1:41, Douglas N. Greve 님이 작성:
>>
>>> It looks like it is failing when computing the partial correlation coef.
>>> Try  running it with --no-pcc
>>>
>>> On 2/16/2022 10:53 AM, 정현우 wrote:
>>>
>>> External Email - Use Caution
>>> Hi Dr. Greve,
>>>
>>> Yes, it seems like the output folder and some output files were created.
>>>
>>> After running the mri_glmfit, 'three_group_comparison.area.lh.glmdir'
>>> folder was created. In the glmdir folder, 'three_group_comparison.area'
>>> folder was created, and the following files were also created: beta.mgh,
>>> dof.dat, eres.mgh, fwhm.dat, mask.mgh, mri_glmfit.log, rstd.mgh, rvar.mgh,
>>> sar1.mgh, surface, and Xg.dat.
>>>
>>> In the 'three_group_comparison.area' folder, the following files were
>>> created: C.dat, F.mgh, gamma.mgh, maxvox.dat, sig.mgh, and z.mgh.
>>>
>>> Do you have any idea what could have been the problem?
>>>
>>> Thanks,
>>> Hyunwoo Jeong
>>>
>>> 2022년 2월 17일 (목) 오전 12:36, Douglas N. Greve 님이
>>> 작성:
>>>
 Did it create the output folder and some output files? I noticed that
 there is a "error: No such file or directory" error 

 On 2/14/2022 8:46 PM, 정현우 wrote:

 External Email - Use Caution
 Hi Dr. Greve,

 Thank you for your reply. I attached the fsgd file, mtx file and the
 Xg.dat file below.

 Hyunwoo Jeong

 2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve 님이
 작성:

> can you send your fsgd file and the Xg.dat file?
>
> On 2/14/2022 1:21 AM, 정현우 wrote:
>
> External Email - Use Caution
> Hello FreeSurfer Developers,
>
> I'm attempting to compare cortical surface area among three groups
> while controlling for estimated total intracranial volume (eTIV), as
> described on the Surface Based Group Analysis tutorial (*MailScanner
> has detected a possible fraud attempt from "secure-web.cisco.com" claiming
> to be*
> https://secure-web.cisco.com/1izEQQFh6WLGMwrM3Xs629it7zOP-XBWBph47XDqbms-H1Hhx9VK2hIANXLHVyeXhhuBWDKPLEeqHMQoZPfVtsiZ_56lBNWGDX7p8Jla8vd-Qdo2Lk83MbbSVulSYEqKW9XHdVqhbZrdGwD4PaJAsASJlOWW3LuFzX7vHd2gCqVhYbh_SCnx1yJ579IJwpKBwHQqIQNjVdg7IoqpJyivJw0mYAqAcfv-ByuUM3T1OEKvD7uA5Db9HW7y0WG8yxpoDF50DneGtK4G9Txk3r_mP_9EfArWuwoOzs1xshdTER3gnQIT1WcdjznrgiiACqnuC3wItlIPr9rt9eU3vGttvKg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0
> 

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

[Douglas N. Greve]

Can you upload the data to me somewhere? I'd need the input volume and 
the fsgd and any contrasts


On 2/21/2022 10:24 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Thank you for your suggestion. Unfortunately, the same problem 
occurred when I ran the command with --no-pcc. Folders and files with 
the same names were created. and the following error message 
(identical to the previous one) appeared.


error: No such file or directory
error: MatrixMultiplyD(): m2 is null
 break 
/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596


Do you have any other suggestions? I appreciate your help so far.

Best,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 10:18, 정현우 님이 작성:

Hi Dr. Greve,

Thank you for your suggestion. Unfortunately, the same problem
occurred when I ran the command with --no-pcc. Folders and files
with the same names were created. and the following error message
(identical to the previous one) appeared.

error: No such file or directory
error: MatrixMultiplyD(): m2 is null
 break

/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596

Do you have any other suggestions? I appreciate your help so far.

Best,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 1:41, Douglas N. Greve
님이 작성:

It looks like it is failing when computing the partial
correlation coef. Try  running it with --no-pcc

On 2/16/2022 10:53 AM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Yes, it seems like the output folder and some output files
were created.

After running the mri_glmfit,
'three_group_comparison.area.lh.glmdir' folder was created.
In the glmdir folder, 'three_group_comparison.area' folder
was created, and the following files were also created:
beta.mgh, dof.dat, eres.mgh, fwhm.dat, mask.mgh,
mri_glmfit.log, rstd.mgh, rvar.mgh, sar1.mgh, surface, and
Xg.dat.

In the 'three_group_comparison.area' folder, the following
files were created: C.dat, F.mgh, gamma.mgh, maxvox.dat,
sig.mgh, and z.mgh.

Do you have any idea what could have been the problem?

Thanks,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 12:36, Douglas N. Greve
님이 작성:

Did it create the output folder and some output files? I
noticed that there is a "error: No such file or
directory" error 

On 2/14/2022 8:46 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Thank you for your reply. I attached the fsgd file, mtx
file and the Xg.dat file below.

Hyunwoo Jeong

2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve
님이 작성:

can you send your fsgd file and the Xg.dat file?

On 2/14/2022 1:21 AM, 정현우 wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to compare cortical surface area
among three groups while controlling for estimated
total intracranial volume (eTIV), as described on
the Surface Based Group Analysis tutorial
(*MailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be*

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0

).


I ran the following command:

mri_glmfit --y
three_group_comparison.area.lh.10.mgh --fsgd
three_group_comparison.area.fsgd dods --C
three_group_comparison.area.mtx --surf fsaverage lh
--cortex --glmdir
three_group_comparison.area.lh.glmdir --eres-save

Then I got the following error:

gdfRead(): reading three_group_comparison.area.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will
NOT be done.
Continuous Variable Means (all subjects)
0 eTIV 1.53351e+06 139455
Class Size and Means of each Continuous Variable
1 0 42 1566070.5417
2 1 34 1515147.1360
3 2 15 1483959.5000
INFO: gd2mtx_method is dods
Reading source surface
/me

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

[정현우]

External Email - Use Caution

Hi Dr. Greve,

Thank you for your suggestion. Unfortunately, the same problem occurred
when I ran the command with --no-pcc. Folders and files with the same names
were created. and the following error message (identical to the previous
one) appeared.

error: No such file or directory
error: MatrixMultiplyD(): m2 is null
 break
/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596

Do you have any other suggestions? I appreciate your help so far.

Best,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 10:18, 정현우 님이 작성:

> Hi Dr. Greve,
>
> Thank you for your suggestion. Unfortunately, the same problem occurred
> when I ran the command with --no-pcc. Folders and files with the same names
> were created. and the following error message (identical to the previous
> one) appeared.
>
> error: No such file or directory
> error: MatrixMultiplyD(): m2 is null
>  break
> /home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596
>
> Do you have any other suggestions? I appreciate your help so far.
>
> Best,
> Hyunwoo Jeong
>
> 2022년 2월 17일 (목) 오전 1:41, Douglas N. Greve 님이 작성:
>
>> It looks like it is failing when computing the partial correlation coef.
>> Try  running it with --no-pcc
>>
>> On 2/16/2022 10:53 AM, 정현우 wrote:
>>
>> External Email - Use Caution
>> Hi Dr. Greve,
>>
>> Yes, it seems like the output folder and some output files were created.
>>
>> After running the mri_glmfit, 'three_group_comparison.area.lh.glmdir'
>> folder was created. In the glmdir folder, 'three_group_comparison.area'
>> folder was created, and the following files were also created: beta.mgh,
>> dof.dat, eres.mgh, fwhm.dat, mask.mgh, mri_glmfit.log, rstd.mgh, rvar.mgh,
>> sar1.mgh, surface, and Xg.dat.
>>
>> In the 'three_group_comparison.area' folder, the following files were
>> created: C.dat, F.mgh, gamma.mgh, maxvox.dat, sig.mgh, and z.mgh.
>>
>> Do you have any idea what could have been the problem?
>>
>> Thanks,
>> Hyunwoo Jeong
>>
>> 2022년 2월 17일 (목) 오전 12:36, Douglas N. Greve 님이
>> 작성:
>>
>>> Did it create the output folder and some output files? I noticed that
>>> there is a "error: No such file or directory" error 
>>>
>>> On 2/14/2022 8:46 PM, 정현우 wrote:
>>>
>>> External Email - Use Caution
>>> Hi Dr. Greve,
>>>
>>> Thank you for your reply. I attached the fsgd file, mtx file and the
>>> Xg.dat file below.
>>>
>>> Hyunwoo Jeong
>>>
>>> 2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve 님이
>>> 작성:
>>>
 can you send your fsgd file and the Xg.dat file?

 On 2/14/2022 1:21 AM, 정현우 wrote:

 External Email - Use Caution
 Hello FreeSurfer Developers,

 I'm attempting to compare cortical surface area among three groups
 while controlling for estimated total intracranial volume (eTIV), as
 described on the Surface Based Group Analysis tutorial (*MailScanner
 has detected a possible fraud attempt from "secure-web.cisco.com" claiming
 to be*
 https://secure-web.cisco.com/1mORL3QNAn5tihhXg5Rlq7F96j6pj7JRpJ_bSOoLiPouSFmLwRTdFe-2M56ZzhTzgPWV0bI-L9OGjw4y5MSTrDTukPfOJmx35AgkxzIXdCTSHK0U4hJ16N5cotKAet0ebN-9Y56mx3pJ5kOStL_2KkR2uTgAO_Q91W2E8NIrLdwKB_72vHUbC_2Mm2dPI6CDbdSvNYj36dP6NjsRP3Hi_q_YIUWJDsbXla1lb8AVGKhpt56FLHhZIth_H5cT2j1WzFmcbTeoVkxPM_oUPEsElIRXkQBE4aJeUxUaTjd5M9lw8oBvnnPai2d1vgOE92kVDzWFkGaJDJcFFrG8C6OiczQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0
 
 ).

 I ran the following command:

 mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd
 three_group_comparison.area.fsgd dods --C three_group_comparison.area.mtx
 --surf fsaverage lh --cortex --glmdir three_group_comparison.area.lh.glmdir
 --eres-save

 Then I got the following error:

 gdfRead(): reading three_group_comparison.area.fsgd
 INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
 Continuous Variable Means (all subjects)
 0 eTIV 1.53351e+06 139455
 Class Size and Means of each Continuous Variable
 1 0 42 1566070.5417
 2 1 34 1515147.1360
 3 2 15 1483959.5000
 INFO: gd2mtx_method is dods
 Reading source surface
 /media/sjkim/hd2/subject_data/fsaverage/surf/lh.white
 Number of vertices 163842
 Number of faces327680
 Total area 65417.00
 AvgVtxArea   0.399269
 AvgVtxDist   0.721953
 StdVtxDist   0.195472

 7.2.0
 cwd /media/sjkim/hd2/subject_data/gl

Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out cortical thickness

[Douglas N. Greve]

Hi Asim, I ran into some issues on my test. I think the software is 
doing what it is supposed to do, but I think there is something wrong 
with the underlying permutation method when using PVRs. This will take a 
while for me to figure out. In the  meantime, you can try using the more 
conventional mcz correction. If the cluster p-value is very strong, then 
the liberalness of the method might not matter.


On 2/22/2022 5:32 PM, Dhungana, Asim wrote:
Thank you! I ran the development version of the mri_glmfit-sim command 
on my data, and it did not crash and seems to give reasonable outputs 
(smaller clusters disappear after correction). Whenever your tests are 
done, it will be good to know if they confirm that everything is working.


Best,
Asim

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Monday, February 21, 2022 6:29 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] mri_glmfit of surface CBF maps while 
regressing out cortical thickness
I just updated the code to accept PVRs. I'm not sure what I have to do 
to test it; I guess I need to run the null test like I did for the 
non-PVR version. This will take a while. In the mean time, can you 
download the development version and just try it on your data to see 
if it crashes or gives results that don't seem to make sense? You'll 
have to wait until the development version is updated (probably tomorrow).



On 2/17/2022 5:22 PM, Dhungana, Asim wrote:
Hello Doug, just following up on my questions below on how/if I can 
correct for multiple comparisons with PVR. Thanks again.


Best,
Asim

*From:* Dhungana, Asim  
<mailto:adhung...@mgh.harvard.edu>

*Sent:* Monday, February 14, 2022 11:45 AM
*To:* Freesurfer support list  
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] mri_glmfit of surface CBF maps while 
regressing out cortical thickness
OK, I see. How would you recommend correcting for multiple 
comparisons if the perm option does not work with PVR?


Also, are you saying that I should only use the glm.osgm.lh/eres.mgh 
file as a pvr argument? Does this look correct:


mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr glm.osgm.lh/eres.mgh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

Best,
Asim

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas 
N. Greve  <mailto:dgr...@mgh.harvard.edu>

*Sent:* Sunday, February 13, 2022 5:29 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
<mailto:freesurfer@nmr.mgh.harvard.edu> 
 <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] mri_glmfit of surface CBF maps while 
regressing out cortical thickness

Re: long run  time. Sorry, permutation will not work with PVR.
Re: mean thickness. Use the eres.mgh from you osgm analysis instead 
of the raw thickness map (lh.thickness.fwhm10.mgh)


On 2/8/2022 4:12 PM, Dhungana, Asim wrote:

Dear Freesurfer experts,

I am trying to run a GLM analysis comparing the difference in the 
cortical CBF maps between two groups, but I would like to regress 
out cortical thickness. I read through a post with a similar 
question 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65059.html 
<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65059.html>), 
but I am still a little confused and want to confirm the steps of my 
analysis below:


---

1. Compile/smooth CBF data on surface for all subjects.
mris_preproc
--hemi lh \
--projfrac 0.5 \
--target fsaverage \
--o lh.cbf.00.mgh \
--iv subj1/cbf.mgz  subj1/register_pasl.dat \
--iv subj2/cbf.mgz  subj2/register_pasl.dat \
... until subjN

mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.cbf.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.cbf.fwhm10.mgh

2. Compile/smooth thickness data on surface for all subjects.
mris_preproc \
--fsgd cbf.fsgd \
--target fsaverage \
--hemi lh \
--meas thickness \
--out lh.thickness.00.mgh

mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.thickness.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.thickness.fwhm10.mgh

3. GLM fit of CBF maps, including thickness as a regressor.
mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr lh.thickness.fwhm10.mgh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

4. Multiple comparisons correction
mri_glmfit-sim \
--glmdir lh.cbf.fwhm10.glmdir \
--perm 1000 1.3 abs \
--cwp 0.05 \
--2spaces \
--bg 35

---

I am currently having issues with Step 4; it has been over

Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out cortical thickness

[Dhungana, Asim]

Thank you! I ran the development version of the mri_glmfit-sim command on my 
data, and it did not crash and seems to give reasonable outputs (smaller 
clusters disappear after correction). Whenever your tests are done, it will be 
good to know if they confirm that everything is working.

Best,
Asim

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Monday, February 21, 2022 6:29 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out 
cortical thickness

I just updated the code to accept PVRs. I'm not sure what I have to do to test 
it; I guess I need to run the null test like I did for the non-PVR version. 
This will take a while. In the mean time, can you download the development 
version and just try it on your data to see if it crashes or gives results that 
don't seem to make sense? You'll have to wait until the development version is 
updated (probably tomorrow).


On 2/17/2022 5:22 PM, Dhungana, Asim wrote:
Hello Doug, just following up on my questions below on how/if I can correct for 
multiple comparisons with PVR. Thanks again.

Best,
Asim

From: Dhungana, Asim 
<mailto:adhung...@mgh.harvard.edu>
Sent: Monday, February 14, 2022 11:45 AM
To: Freesurfer support list 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out 
cortical thickness

OK, I see. How would you recommend correcting for multiple comparisons if the 
perm option does not work with PVR?

Also, are you saying that I should only use the glm.osgm.lh/eres.mgh file as a 
pvr argument? Does this look correct:

mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr glm.osgm.lh/eres.mgh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

Best,
Asim

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Sent: Sunday, February 13, 2022 5:29 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out 
cortical thickness

Re: long run  time. Sorry, permutation will not work with PVR.
Re: mean thickness. Use the eres.mgh from you osgm analysis instead of the raw 
thickness map (lh.thickness.fwhm10.mgh)

On 2/8/2022 4:12 PM, Dhungana, Asim wrote:
Dear Freesurfer experts,

I am trying to run a GLM analysis comparing the difference in the cortical CBF 
maps between two groups, but I would like to regress out cortical thickness. I 
read through a post with a similar question 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65059.html), 
but I am still a little confused and want to confirm the steps of my analysis 
below:

---

1. Compile/smooth CBF data on surface for all subjects.
mris_preproc
--hemi lh \
--projfrac 0.5 \
--target fsaverage \
--o lh.cbf.00.mgh \
--iv subj1/cbf.mgz  subj1/register_pasl.dat \
--iv subj2/cbf.mgz  subj2/register_pasl.dat \
... until subjN

mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.cbf.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.cbf.fwhm10.mgh

2. Compile/smooth thickness data on surface for all subjects.
mris_preproc \
--fsgd cbf.fsgd \
--target fsaverage \
--hemi lh \
--meas thickness \
--out lh.thickness.00.mgh

mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.thickness.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.thickness.fwhm10.mgh

3. GLM fit of CBF maps, including thickness as a regressor.
mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr lh.thickness.fwhm10.mgh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

4. Multiple comparisons correction
mri_glmfit-sim \
--glmdir lh.cbf.fwhm10.glmdir \
--perm 1000 1.3 abs \
--cwp 0.05 \
--2spaces \
--bg 35

---

I am currently having issues with Step 4; it has been over an hour, and it 
seems that the command will not finish executing. It is also not outputting any 
error messages. Whenever I run this analysis using the same parameters but 
without regressing out thickness, this step takes under five minutes on my 
machine and returns appropriate results. It seems like I must be doing 
something wrong, but I'm not sure. Please let me know if there is anything that 
you would change/add above.

Also, I noticed that you recommended regressing out the overall mean thickness 
(which you can obtain through mri_glmfit --surf fsaverage lh --osgm --y 
lh.thickness.fwhm10.mgh --o glm.osgm.lh --eres-save). Is glm.osgm.lh the mean 
stratified by class or the

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

[정현우]

External Email - Use Caution

Hi Dr. Greve,

Thank you for your suggestion. Unfortunately, the same problem occurred
when I ran the command with --no-pcc. Folders and files with the same names
were created. and the following error message (identical to the previous
one) appeared.

error: No such file or directory
error: MatrixMultiplyD(): m2 is null
 break
/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596

Do you have any other suggestions? I appreciate your help so far.

Best,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 10:18, 정현우 님이 작성:

> Hi Dr. Greve,
>
> Thank you for your suggestion. Unfortunately, the same problem occurred
> when I ran the command with --no-pcc. Folders and files with the same names
> were created. and the following error message (identical to the previous
> one) appeared.
>
> error: No such file or directory
> error: MatrixMultiplyD(): m2 is null
>  break
> /home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596
>
> Do you have any other suggestions? I appreciate your help so far.
>
> Best,
> Hyunwoo Jeong
>
> 2022년 2월 17일 (목) 오전 1:41, Douglas N. Greve 님이 작성:
>
>> It looks like it is failing when computing the partial correlation coef.
>> Try  running it with --no-pcc
>>
>> On 2/16/2022 10:53 AM, 정현우 wrote:
>>
>> External Email - Use Caution
>> Hi Dr. Greve,
>>
>> Yes, it seems like the output folder and some output files were created.
>>
>> After running the mri_glmfit, 'three_group_comparison.area.lh.glmdir'
>> folder was created. In the glmdir folder, 'three_group_comparison.area'
>> folder was created, and the following files were also created: beta.mgh,
>> dof.dat, eres.mgh, fwhm.dat, mask.mgh, mri_glmfit.log, rstd.mgh, rvar.mgh,
>> sar1.mgh, surface, and Xg.dat.
>>
>> In the 'three_group_comparison.area' folder, the following files were
>> created: C.dat, F.mgh, gamma.mgh, maxvox.dat, sig.mgh, and z.mgh.
>>
>> Do you have any idea what could have been the problem?
>>
>> Thanks,
>> Hyunwoo Jeong
>>
>> 2022년 2월 17일 (목) 오전 12:36, Douglas N. Greve 님이
>> 작성:
>>
>>> Did it create the output folder and some output files? I noticed that
>>> there is a "error: No such file or directory" error 
>>>
>>> On 2/14/2022 8:46 PM, 정현우 wrote:
>>>
>>> External Email - Use Caution
>>> Hi Dr. Greve,
>>>
>>> Thank you for your reply. I attached the fsgd file, mtx file and the
>>> Xg.dat file below.
>>>
>>> Hyunwoo Jeong
>>>
>>> 2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve 님이
>>> 작성:
>>>
 can you send your fsgd file and the Xg.dat file?

 On 2/14/2022 1:21 AM, 정현우 wrote:

 External Email - Use Caution
 Hello FreeSurfer Developers,

 I'm attempting to compare cortical surface area among three groups
 while controlling for estimated total intracranial volume (eTIV), as
 described on the Surface Based Group Analysis tutorial (*MailScanner
 has detected a possible fraud attempt from "secure-web.cisco.com" claiming
 to be*
 https://secure-web.cisco.com/1204iDDV1u7dfgPjlvMCojX7zfEl2iiQ3ixQk7biOTrhu_OLNhVRoMb3-_9IL51WZchsVTQL3Xl2ep1WmonpfuoLnsNzaNyZE6POjDWR7F43Ocx1HXqJ3buXdsOts4xnyCOZn2uDC0ZwxTXouox5AgHCe0L0rwbax01pGNc0Vj8oj07tkxgRMIrbtLziYHDDFeLV3drvvwVcklcs_y70cuUORoIgCNVyFqPKidXpEvkp4P0CFJCPlDxXIbtWpeJBi4jC5ENwo44HOBK_JP3UJrgKCWrlRsZ7SJvDsRv2lK7GnfwiKAcrZlhWDFuiKfdXF/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0
 
 ).

 I ran the following command:

 mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd
 three_group_comparison.area.fsgd dods --C three_group_comparison.area.mtx
 --surf fsaverage lh --cortex --glmdir three_group_comparison.area.lh.glmdir
 --eres-save

 Then I got the following error:

 gdfRead(): reading three_group_comparison.area.fsgd
 INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
 Continuous Variable Means (all subjects)
 0 eTIV 1.53351e+06 139455
 Class Size and Means of each Continuous Variable
 1 0 42 1566070.5417
 2 1 34 1515147.1360
 3 2 15 1483959.5000
 INFO: gd2mtx_method is dods
 Reading source surface
 /media/sjkim/hd2/subject_data/fsaverage/surf/lh.white
 Number of vertices 163842
 Number of faces327680
 Total area 65417.00
 AvgVtxArea   0.399269
 AvgVtxDist   0.721953
 StdVtxDist   0.195472

 7.2.0
 cwd /media/sjkim/hd2/subject_data/glm
 cmdline mri_glm

Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out cortical thickness

[Douglas N. Greve]

I just updated the code to accept PVRs. I'm not sure what I have to do 
to test it; I guess I need to run the null test like I did for the 
non-PVR version. This will take a while. In the mean time, can you 
download the development version and just try it on your data to see if 
it crashes or gives results that don't seem to make sense? You'll have 
to wait until the development version is updated (probably tomorrow).



On 2/17/2022 5:22 PM, Dhungana, Asim wrote:
Hello Doug, just following up on my questions below on how/if I can 
correct for multiple comparisons with PVR. Thanks again.


Best,
Asim

*From:* Dhungana, Asim 
*Sent:* Monday, February 14, 2022 11:45 AM
*To:* Freesurfer support list 
*Subject:* Re: [Freesurfer] mri_glmfit of surface CBF maps while 
regressing out cortical thickness
OK, I see. How would you recommend correcting for multiple comparisons 
if the perm option does not work with PVR?


Also, are you saying that I should only use the glm.osgm.lh/eres.mgh 
file as a pvr argument? Does this look correct:


mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr glm.osgm.lh/eres.mgh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

Best,
Asim

*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Sunday, February 13, 2022 5:29 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] mri_glmfit of surface CBF maps while 
regressing out cortical thickness

Re: long run  time. Sorry, permutation will not work with PVR.
Re: mean thickness. Use the eres.mgh from you osgm analysis instead of 
the raw thickness map (lh.thickness.fwhm10.mgh)


On 2/8/2022 4:12 PM, Dhungana, Asim wrote:

Dear Freesurfer experts,

I am trying to run a GLM analysis comparing the difference in the 
cortical CBF maps between two groups, but I would like to regress out 
cortical thickness. I read through a post with a similar question 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65059.html 
<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65059.html>), 
but I am still a little confused and want to confirm the steps of my 
analysis below:


---

1. Compile/smooth CBF data on surface for all subjects.
mris_preproc
--hemi lh \
--projfrac 0.5 \
--target fsaverage \
--o lh.cbf.00.mgh \
--iv subj1/cbf.mgz  subj1/register_pasl.dat \
--iv subj2/cbf.mgz  subj2/register_pasl.dat \
... until subjN

mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.cbf.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.cbf.fwhm10.mgh

2. Compile/smooth thickness data on surface for all subjects.
mris_preproc \
--fsgd cbf.fsgd \
--target fsaverage \
--hemi lh \
--meas thickness \
--out lh.thickness.00.mgh

mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.thickness.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.thickness.fwhm10.mgh

3. GLM fit of CBF maps, including thickness as a regressor.
mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr lh.thickness.fwhm10.mgh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

4. Multiple comparisons correction
mri_glmfit-sim \
--glmdir lh.cbf.fwhm10.glmdir \
--perm 1000 1.3 abs \
--cwp 0.05 \
--2spaces \
--bg 35

---

I am currently having issues with Step 4; it has been over an hour, 
and it seems that the command will not finish executing. It is also 
not outputting any error messages. Whenever I run this analysis using 
the same parameters but without regressing out thickness, this step 
takes under five minutes on my machine and returns appropriate 
results. It seems like I must be doing something wrong, but I'm not 
sure. Please let me know if there is anything that you would 
change/add above.


Also, I noticed that you recommended regressing out the overall mean 
thickness (which you can obtain through mri_glmfit --surf fsaverage 
lh --osgm --y lh.thickness.fwhm10.mgh --o glm.osgm.lh --eres-save). 
Is glm.osgm.lh the mean stratified by class or the overall mean? If I 
were to include this in my GLM fit, would this be the correct command:


mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr lh.thickness.fwhm10.mgh glm.osgm.lh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

Thank you for taking a look at this, let me know if you need any 
other information.


Best,
Asim Dhungana

​Freesurfer version: 
freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b


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Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out cortical thickness

[Dhungana, Asim]

Hello Doug, just following up on my questions below on how/if I can correct for 
multiple comparisons with PVR. Thanks again.

Best,
Asim

From: Dhungana, Asim 
Sent: Monday, February 14, 2022 11:45 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out 
cortical thickness

OK, I see. How would you recommend correcting for multiple comparisons if the 
perm option does not work with PVR?

Also, are you saying that I should only use the glm.osgm.lh/eres.mgh file as a 
pvr argument? Does this look correct:

mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr glm.osgm.lh/eres.mgh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

Best,
Asim

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Sunday, February 13, 2022 5:29 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out 
cortical thickness

Re: long run  time. Sorry, permutation will not work with PVR.
Re: mean thickness. Use the eres.mgh from you osgm analysis instead of the raw 
thickness map (lh.thickness.fwhm10.mgh)

On 2/8/2022 4:12 PM, Dhungana, Asim wrote:
Dear Freesurfer experts,

I am trying to run a GLM analysis comparing the difference in the cortical CBF 
maps between two groups, but I would like to regress out cortical thickness. I 
read through a post with a similar question 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65059.html), 
but I am still a little confused and want to confirm the steps of my analysis 
below:

---

1. Compile/smooth CBF data on surface for all subjects.
mris_preproc
--hemi lh \
--projfrac 0.5 \
--target fsaverage \
--o lh.cbf.00.mgh \
--iv subj1/cbf.mgz  subj1/register_pasl.dat \
--iv subj2/cbf.mgz  subj2/register_pasl.dat \
... until subjN

mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.cbf.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.cbf.fwhm10.mgh

2. Compile/smooth thickness data on surface for all subjects.
mris_preproc \
--fsgd cbf.fsgd \
--target fsaverage \
--hemi lh \
--meas thickness \
--out lh.thickness.00.mgh

mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.thickness.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.thickness.fwhm10.mgh

3. GLM fit of CBF maps, including thickness as a regressor.
mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr lh.thickness.fwhm10.mgh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

4. Multiple comparisons correction
mri_glmfit-sim \
--glmdir lh.cbf.fwhm10.glmdir \
--perm 1000 1.3 abs \
--cwp 0.05 \
--2spaces \
--bg 35

---

I am currently having issues with Step 4; it has been over an hour, and it 
seems that the command will not finish executing. It is also not outputting any 
error messages. Whenever I run this analysis using the same parameters but 
without regressing out thickness, this step takes under five minutes on my 
machine and returns appropriate results. It seems like I must be doing 
something wrong, but I'm not sure. Please let me know if there is anything that 
you would change/add above.

Also, I noticed that you recommended regressing out the overall mean thickness 
(which you can obtain through mri_glmfit --surf fsaverage lh --osgm --y 
lh.thickness.fwhm10.mgh --o glm.osgm.lh --eres-save). Is glm.osgm.lh the mean 
stratified by class or the overall mean? If I were to include this in my GLM 
fit, would this be the correct command:

mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr lh.thickness.fwhm10.mgh glm.osgm.lh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

Thank you for taking a look at this, let me know if you need any other 
information.

Best,
Asim Dhungana

​Freesurfer version: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b



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Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

[정현우]

External Email - Use Caution

Hi Dr. Greve,

Thank you for your suggestion. Unfortunately, the same problem occurred
when I ran the command with --no-pcc. Folders and files with the same names
were created. and the following error message (identical to the previous
one) appeared.

error: No such file or directory
error: MatrixMultiplyD(): m2 is null
 break
/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596

Do you have any other suggestions? I appreciate your help so far.

Best,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 1:41, Douglas N. Greve 님이 작성:

> It looks like it is failing when computing the partial correlation coef.
> Try  running it with --no-pcc
>
> On 2/16/2022 10:53 AM, 정현우 wrote:
>
> External Email - Use Caution
> Hi Dr. Greve,
>
> Yes, it seems like the output folder and some output files were created.
>
> After running the mri_glmfit, 'three_group_comparison.area.lh.glmdir'
> folder was created. In the glmdir folder, 'three_group_comparison.area'
> folder was created, and the following files were also created: beta.mgh,
> dof.dat, eres.mgh, fwhm.dat, mask.mgh, mri_glmfit.log, rstd.mgh, rvar.mgh,
> sar1.mgh, surface, and Xg.dat.
>
> In the 'three_group_comparison.area' folder, the following files were
> created: C.dat, F.mgh, gamma.mgh, maxvox.dat, sig.mgh, and z.mgh.
>
> Do you have any idea what could have been the problem?
>
> Thanks,
> Hyunwoo Jeong
>
> 2022년 2월 17일 (목) 오전 12:36, Douglas N. Greve 님이 작성:
>
>> Did it create the output folder and some output files? I noticed that
>> there is a "error: No such file or directory" error 
>>
>> On 2/14/2022 8:46 PM, 정현우 wrote:
>>
>> External Email - Use Caution
>> Hi Dr. Greve,
>>
>> Thank you for your reply. I attached the fsgd file, mtx file and the
>> Xg.dat file below.
>>
>> Hyunwoo Jeong
>>
>> 2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve 님이 작성:
>>
>>> can you send your fsgd file and the Xg.dat file?
>>>
>>> On 2/14/2022 1:21 AM, 정현우 wrote:
>>>
>>> External Email - Use Caution
>>> Hello FreeSurfer Developers,
>>>
>>> I'm attempting to compare cortical surface area among three groups while
>>> controlling for estimated total intracranial volume (eTIV), as described on
>>> the Surface Based Group Analysis tutorial (*MailScanner has detected a
>>> possible fraud attempt from "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/1JGKOGG3EbAGg7qWjLbX8YmiC0SOUsSTJEQIi-zahadD2Ewv_xTY8mcg_Xe3PPbFG9UcuM7vmfwX44gM9OfJRLTcft6W63a1afrF9eQ0v4JZOSIzGU4EEEqoMUgpyYGmJnhLMQowNp9XUfW9y4RCawbybVcUpZqJgvPT3aXudQkrhTgWAzFHqCoPodTx4S3AMDcMVbryMldwEBY5w-mr_Of5_f1JHOVzBNtxu6lHfe1ifLQ37njgRAMyfsjT7zc2HBZqOyIhTss0tXUt20Uf0fABQdoxU0o7TBr8roQKoorHbAkCDegu_hM08yQDNKSStqgHj31wAoIxodg-XISgO5A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0
>>> 
>>> ).
>>>
>>> I ran the following command:
>>>
>>> mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd
>>> three_group_comparison.area.fsgd dods --C three_group_comparison.area.mtx
>>> --surf fsaverage lh --cortex --glmdir three_group_comparison.area.lh.glmdir
>>> --eres-save
>>>
>>> Then I got the following error:
>>>
>>> gdfRead(): reading three_group_comparison.area.fsgd
>>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>>> Continuous Variable Means (all subjects)
>>> 0 eTIV 1.53351e+06 139455
>>> Class Size and Means of each Continuous Variable
>>> 1 0 42 1566070.5417
>>> 2 1 34 1515147.1360
>>> 3 2 15 1483959.5000
>>> INFO: gd2mtx_method is dods
>>> Reading source surface
>>> /media/sjkim/hd2/subject_data/fsaverage/surf/lh.white
>>> Number of vertices 163842
>>> Number of faces327680
>>> Total area 65417.00
>>> AvgVtxArea   0.399269
>>> AvgVtxDist   0.721953
>>> StdVtxDist   0.195472
>>>
>>> 7.2.0
>>> cwd /media/sjkim/hd2/subject_data/glm
>>> cmdline mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd
>>> three_group_comparison.area.fsgd dods --C three_group_comparison.area.mtx
>>> --surf fsaverage lh --cortex --glmdir three_group_comparison.area.lh.glmdir
>>> --eres-save
>>> sysname  Linux
>>> hostname sjkim-System-Product-Name
>>> machine  x86_64
>>> user sjkim
>>> FixVertexAreaFlag = 1
>>> UseMaskWithSmoothing 1
>>> OneSampleGroupMean 0
>>> y
>>>  /media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh
>>> logyflag 0
>>> usedti  0
>>> FSGD three_group_comparison.area.fsgd
>>> labelmask  /media/sjkim/hd2/subject_data/fsaverage/label/lh.cortex.label
>>> maskinv 0
>>> 

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

[Douglas N. Greve]

It looks like it is failing when computing the partial correlation coef. 
Try  running it with --no-pcc


On 2/16/2022 10:53 AM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Yes, it seems like the output folder and some output files were created.

After running the mri_glmfit, 'three_group_comparison.area.lh.glmdir' 
folder was created. In the glmdir folder, 
'three_group_comparison.area' folder was created, and the following 
files were also created: beta.mgh, dof.dat, eres.mgh, fwhm.dat, 
mask.mgh, mri_glmfit.log, rstd.mgh, rvar.mgh, sar1.mgh, surface, and 
Xg.dat.


In the 'three_group_comparison.area' folder, the following files were 
created: C.dat, F.mgh, gamma.mgh, maxvox.dat, sig.mgh, and z.mgh.


Do you have any idea what could have been the problem?

Thanks,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 12:36, Douglas N. Greve 
님이 작성:


Did it create the output folder and some output files? I noticed
that there is a "error: No such file or directory" error 

On 2/14/2022 8:46 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Thank you for your reply. I attached the fsgd file, mtx file and
the Xg.dat file below.

Hyunwoo Jeong

2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve
님이 작성:

can you send your fsgd file and the Xg.dat file?

On 2/14/2022 1:21 AM, 정현우 wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to compare cortical surface area among three
groups while controlling for estimated total intracranial
volume (eTIV), as described on the Surface Based Group
Analysis tutorial (*MailScanner has detected a possible
fraud attempt from "secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0

).


I ran the following command:

mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd
three_group_comparison.area.fsgd dods --C
three_group_comparison.area.mtx --surf fsaverage lh --cortex
--glmdir three_group_comparison.area.lh.glmdir --eres-save

Then I got the following error:

gdfRead(): reading three_group_comparison.area.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 eTIV 1.53351e+06 139455
Class Size and Means of each Continuous Variable
1 0 42 1566070.5417
2 1 34 1515147.1360
3 2 15 1483959.5000
INFO: gd2mtx_method is dods
Reading source surface
/media/sjkim/hd2/subject_data/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces    327680
Total area         65417.00
AvgVtxArea       0.399269
AvgVtxDist       0.721953
StdVtxDist       0.195472

7.2.0
cwd /media/sjkim/hd2/subject_data/glm
cmdline mri_glmfit --y three_group_comparison.area.lh.10.mgh
--fsgd three_group_comparison.area.fsgd dods --C
three_group_comparison.area.mtx --surf fsaverage lh --cortex
--glmdir three_group_comparison.area.lh.glmdir --eres-save
sysname  Linux
hostname sjkim-System-Product-Name
machine  x86_64
user     sjkim
FixVertexAreaFlag = 1
UseMaskWithSmoothing     1
OneSampleGroupMean 0
y
 /media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh
logyflag 0
usedti  0
FSGD three_group_comparison.area.fsgd
labelmask
 /media/sjkim/hd2/subject_data/fsaverage/label/lh.cortex.label
maskinv 0
glmdir three_group_comparison.area.lh.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory three_group_comparison.area.lh.glmdir
Loading y from
/media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh
   ... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to
three_group_comparison.area.lh.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 833.575
Matrix condition is 1e+08
Found 149955 points in label.
Pruning voxels by thr: 1.175494e-38
Found 149953 voxels in mask
Saving mask to three_group_comparison.area.lh.glmdir/mask.mgh
Reshaping mriglm->mask...
search space = 74612.059149
D

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

[정현우]

External Email - Use Caution

Hi Dr. Greve,

Yes, it seems like the output folder and some output files were created.

After running the mri_glmfit, 'three_group_comparison.area.lh.glmdir'
folder was created. In the glmdir folder, 'three_group_comparison.area'
folder was created, and the following files were also created: beta.mgh,
dof.dat, eres.mgh, fwhm.dat, mask.mgh, mri_glmfit.log, rstd.mgh, rvar.mgh,
sar1.mgh, surface, and Xg.dat.

In the 'three_group_comparison.area' folder, the following files were
created: C.dat, F.mgh, gamma.mgh, maxvox.dat, sig.mgh, and z.mgh.

Do you have any idea what could have been the problem?

Thanks,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 12:36, Douglas N. Greve 님이 작성:

> Did it create the output folder and some output files? I noticed that
> there is a "error: No such file or directory" error 
>
> On 2/14/2022 8:46 PM, 정현우 wrote:
>
> External Email - Use Caution
> Hi Dr. Greve,
>
> Thank you for your reply. I attached the fsgd file, mtx file and the
> Xg.dat file below.
>
> Hyunwoo Jeong
>
> 2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve 님이 작성:
>
>> can you send your fsgd file and the Xg.dat file?
>>
>> On 2/14/2022 1:21 AM, 정현우 wrote:
>>
>> External Email - Use Caution
>> Hello FreeSurfer Developers,
>>
>> I'm attempting to compare cortical surface area among three groups while
>> controlling for estimated total intracranial volume (eTIV), as described on
>> the Surface Based Group Analysis tutorial (*MailScanner has detected a
>> possible fraud attempt from "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1duGCJ8g5oDH3kWtV2kE_IgOGbDv-Z7Oo1gugv3XGOPXCC_aHdLHeX_zWXCHyKuJTkhfKuLFJtTDCYzVitgEvcVchnOFddw57_ZJLQoy0-g2GSfjMtY0GaGQDOOed0PMy0iPrA3jB3gq2wx5hD3SExMDjKcx5lU881z3dQUOs-_kjzPapCw8TJr-brYJqmsshYuuweI_6hU6aixWkmw2o_yQSDK9be99hU89ZEV-lJkESCYdvWyl-8MW8ksqKo3V2WDdcU6gwnVMvOiFnCPc3QTSuMZnwinjJyETm_qhtviOSLT_aygP3eptRkxXNZdVLSIuhDFG55Q0BXXRCMvsGIg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0
>> 
>> ).
>>
>> I ran the following command:
>>
>> mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd
>> three_group_comparison.area.fsgd dods --C three_group_comparison.area.mtx
>> --surf fsaverage lh --cortex --glmdir three_group_comparison.area.lh.glmdir
>> --eres-save
>>
>> Then I got the following error:
>>
>> gdfRead(): reading three_group_comparison.area.fsgd
>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>> Continuous Variable Means (all subjects)
>> 0 eTIV 1.53351e+06 139455
>> Class Size and Means of each Continuous Variable
>> 1 0 42 1566070.5417
>> 2 1 34 1515147.1360
>> 3 2 15 1483959.5000
>> INFO: gd2mtx_method is dods
>> Reading source surface
>> /media/sjkim/hd2/subject_data/fsaverage/surf/lh.white
>> Number of vertices 163842
>> Number of faces327680
>> Total area 65417.00
>> AvgVtxArea   0.399269
>> AvgVtxDist   0.721953
>> StdVtxDist   0.195472
>>
>> 7.2.0
>> cwd /media/sjkim/hd2/subject_data/glm
>> cmdline mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd
>> three_group_comparison.area.fsgd dods --C three_group_comparison.area.mtx
>> --surf fsaverage lh --cortex --glmdir three_group_comparison.area.lh.glmdir
>> --eres-save
>> sysname  Linux
>> hostname sjkim-System-Product-Name
>> machine  x86_64
>> user sjkim
>> FixVertexAreaFlag = 1
>> UseMaskWithSmoothing 1
>> OneSampleGroupMean 0
>> y
>>  /media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh
>> logyflag 0
>> usedti  0
>> FSGD three_group_comparison.area.fsgd
>> labelmask  /media/sjkim/hd2/subject_data/fsaverage/label/lh.cortex.label
>> maskinv 0
>> glmdir three_group_comparison.area.lh.glmdir
>> IllCondOK 0
>> ReScaleX 1
>> DoFFx 0
>> Creating output directory three_group_comparison.area.lh.glmdir
>> Loading y from
>> /media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh
>>... done reading.
>> INFO: gd2mtx_method is dods
>> Saving design matrix to three_group_comparison.area.lh.glmdir/Xg.dat
>> Computing normalized matrix
>> Normalized matrix condition is 833.575
>> Matrix condition is 1e+08
>> Found 149955 points in label.
>> Pruning voxels by thr: 1.175494e-38
>> Found 149953 voxels in mask
>> Saving mask to three_group_comparison.area.lh.glmdir/mask.mgh
>> Reshaping mriglm->mask...
>> search space = 74612.059149
>> DOF = 85
>> Starting fit and test
>> Fit completed in 0.0373833 minutes
>> Computing spatial AR1 on surface
>> Residual: ar1mn=0.997826, ar1std=0.00088

Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

[Douglas N. Greve]

Did it create the output folder and some output files? I noticed that 
there is a "error: No such file or directory" error 


On 2/14/2022 8:46 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

Thank you for your reply. I attached the fsgd file, mtx file and the 
Xg.dat file below.


Hyunwoo Jeong

2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve 
님이 작성:


can you send your fsgd file and the Xg.dat file?

On 2/14/2022 1:21 AM, 정현우 wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to compare cortical surface area among three
groups while controlling for estimated total intracranial volume
(eTIV), as described on the Surface Based Group Analysis tutorial
(*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0

).


I ran the following command:

mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd
three_group_comparison.area.fsgd dods --C
three_group_comparison.area.mtx --surf fsaverage lh --cortex
--glmdir three_group_comparison.area.lh.glmdir --eres-save

Then I got the following error:

gdfRead(): reading three_group_comparison.area.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 eTIV 1.53351e+06 139455
Class Size and Means of each Continuous Variable
1 0 42 1566070.5417
2 1 34 1515147.1360
3 2 15 1483959.5000
INFO: gd2mtx_method is dods
Reading source surface
/media/sjkim/hd2/subject_data/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces    327680
Total area         65417.00
AvgVtxArea       0.399269
AvgVtxDist       0.721953
StdVtxDist       0.195472

7.2.0
cwd /media/sjkim/hd2/subject_data/glm
cmdline mri_glmfit --y three_group_comparison.area.lh.10.mgh
--fsgd three_group_comparison.area.fsgd dods --C
three_group_comparison.area.mtx --surf fsaverage lh --cortex
--glmdir three_group_comparison.area.lh.glmdir --eres-save
sysname  Linux
hostname sjkim-System-Product-Name
machine  x86_64
user     sjkim
FixVertexAreaFlag = 1
UseMaskWithSmoothing     1
OneSampleGroupMean 0
y
 /media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh
logyflag 0
usedti  0
FSGD three_group_comparison.area.fsgd
labelmask
 /media/sjkim/hd2/subject_data/fsaverage/label/lh.cortex.label
maskinv 0
glmdir three_group_comparison.area.lh.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory three_group_comparison.area.lh.glmdir
Loading y from
/media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh
   ... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to three_group_comparison.area.lh.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 833.575
Matrix condition is 1e+08
Found 149955 points in label.
Pruning voxels by thr: 1.175494e-38
Found 149953 voxels in mask
Saving mask to three_group_comparison.area.lh.glmdir/mask.mgh
Reshaping mriglm->mask...
search space = 74612.059149
DOF = 85
Starting fit and test
Fit completed in 0.0373833 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.997826, ar1std=0.000886, gstd=8.674183,
fwhm=20.426140
Writing results
  three_group_comparison.area
    maxvox sig=3.0263  F=7.57212  at  index 107440 0 0  
 seed=1645215319
error: No such file or directory
error: MatrixMultiplyD(): m2 is null
 break

/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596

I used FreeSurfer version 7.2.0 and Ubuntu 20.04.

I've searched the mail archives and similar errors have been
reported in qdec, but I could not find any specific solution for
this problem. Do you have any suggestions to solve this problem?

Thank you in advance,

Hyunwoo Jeong

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Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

[정현우]

External Email - Use Caution

Hi Dr. Greve,

Thank you for your reply. I attached the fsgd file, mtx file and the Xg.dat
file below.

Hyunwoo Jeong

2022년 2월 15일 (화) 오전 1:21, Douglas N. Greve 님이 작성:

> can you send your fsgd file and the Xg.dat file?
>
> On 2/14/2022 1:21 AM, 정현우 wrote:
>
> External Email - Use Caution
> Hello FreeSurfer Developers,
>
> I'm attempting to compare cortical surface area among three groups while
> controlling for estimated total intracranial volume (eTIV), as described on
> the Surface Based Group Analysis tutorial (*MailScanner has detected a
> possible fraud attempt from "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1czZRw3EoQx6OvftUtPfBxAe8r0M8EZljAEkQmJk1CUdUwVeyBC5XdwccaJukFkj11JSC3rz-4tyXamEaWMTikD43VqkZe3Wrpy-2GcwBeX2w_joRuTh_pbh5A5mpTSm2j-x1w5OnT9UY_mkXIIOrJObGDmx0C3NRfDh2N3WRW5UwYjk4UgXaNQDG52Un3_RjntVjT1IgSdJRooVPNfxqzm-aRfuT9iwwhxdFzZD3CU2Z2f_TJV5cZgVMhPQI9bGBhj7MVsTTD8CBN35Qd_bdwcqODbZc2HEENCLIta0xByr_8Zqrw-0pSBCFAebnlHKWHZwCwHNFmTYrBc6YKuv59g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0
> 
> ).
>
> I ran the following command:
>
> mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd
> three_group_comparison.area.fsgd dods --C three_group_comparison.area.mtx
> --surf fsaverage lh --cortex --glmdir three_group_comparison.area.lh.glmdir
> --eres-save
>
> Then I got the following error:
>
> gdfRead(): reading three_group_comparison.area.fsgd
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> Continuous Variable Means (all subjects)
> 0 eTIV 1.53351e+06 139455
> Class Size and Means of each Continuous Variable
> 1 0 42 1566070.5417
> 2 1 34 1515147.1360
> 3 2 15 1483959.5000
> INFO: gd2mtx_method is dods
> Reading source surface
> /media/sjkim/hd2/subject_data/fsaverage/surf/lh.white
> Number of vertices 163842
> Number of faces327680
> Total area 65417.00
> AvgVtxArea   0.399269
> AvgVtxDist   0.721953
> StdVtxDist   0.195472
>
> 7.2.0
> cwd /media/sjkim/hd2/subject_data/glm
> cmdline mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd
> three_group_comparison.area.fsgd dods --C three_group_comparison.area.mtx
> --surf fsaverage lh --cortex --glmdir three_group_comparison.area.lh.glmdir
> --eres-save
> sysname  Linux
> hostname sjkim-System-Product-Name
> machine  x86_64
> user sjkim
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 0
> y
>  /media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh
> logyflag 0
> usedti  0
> FSGD three_group_comparison.area.fsgd
> labelmask  /media/sjkim/hd2/subject_data/fsaverage/label/lh.cortex.label
> maskinv 0
> glmdir three_group_comparison.area.lh.glmdir
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
> Creating output directory three_group_comparison.area.lh.glmdir
> Loading y from
> /media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh
>... done reading.
> INFO: gd2mtx_method is dods
> Saving design matrix to three_group_comparison.area.lh.glmdir/Xg.dat
> Computing normalized matrix
> Normalized matrix condition is 833.575
> Matrix condition is 1e+08
> Found 149955 points in label.
> Pruning voxels by thr: 1.175494e-38
> Found 149953 voxels in mask
> Saving mask to three_group_comparison.area.lh.glmdir/mask.mgh
> Reshaping mriglm->mask...
> search space = 74612.059149
> DOF = 85
> Starting fit and test
> Fit completed in 0.0373833 minutes
> Computing spatial AR1 on surface
> Residual: ar1mn=0.997826, ar1std=0.000886, gstd=8.674183, fwhm=20.426140
> Writing results
>   three_group_comparison.area
> maxvox sig=3.0263  F=7.57212  at  index 107440 0 0seed=1645215319
> error: No such file or directory
> error: MatrixMultiplyD(): m2 is null
>  break
> /home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596
>
> I used FreeSurfer version 7.2.0 and Ubuntu 20.04.
>
> I've searched the mail archives and similar errors have been reported in
> qdec, but I could not find any specific solution for this problem. Do you
> have any suggestions to solve this problem?
>
> Thank you in advance,
>
> Hyunwoo Jeong
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1e2hDU-pnYJe1fZTYbCeBlfK68223y1O5DfBiwonrp

Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out cortical thickness

[Dhungana, Asim]

OK, I see. How would you recommend correcting for multiple comparisons if the 
perm option does not work with PVR?

Also, are you saying that I should only use the glm.osgm.lh/eres.mgh file as a 
pvr argument? Does this look correct:

mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr glm.osgm.lh/eres.mgh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

Best,
Asim

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Sunday, February 13, 2022 5:29 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out 
cortical thickness

Re: long run  time. Sorry, permutation will not work with PVR.
Re: mean thickness. Use the eres.mgh from you osgm analysis instead of the raw 
thickness map (lh.thickness.fwhm10.mgh)

On 2/8/2022 4:12 PM, Dhungana, Asim wrote:
Dear Freesurfer experts,

I am trying to run a GLM analysis comparing the difference in the cortical CBF 
maps between two groups, but I would like to regress out cortical thickness. I 
read through a post with a similar question 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65059.html), 
but I am still a little confused and want to confirm the steps of my analysis 
below:

---

1. Compile/smooth CBF data on surface for all subjects.
mris_preproc
--hemi lh \
--projfrac 0.5 \
--target fsaverage \
--o lh.cbf.00.mgh \
--iv subj1/cbf.mgz  subj1/register_pasl.dat \
--iv subj2/cbf.mgz  subj2/register_pasl.dat \
... until subjN

mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.cbf.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.cbf.fwhm10.mgh

2. Compile/smooth thickness data on surface for all subjects.
mris_preproc \
--fsgd cbf.fsgd \
--target fsaverage \
--hemi lh \
--meas thickness \
--out lh.thickness.00.mgh

mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.thickness.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.thickness.fwhm10.mgh

3. GLM fit of CBF maps, including thickness as a regressor.
mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr lh.thickness.fwhm10.mgh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

4. Multiple comparisons correction
mri_glmfit-sim \
--glmdir lh.cbf.fwhm10.glmdir \
--perm 1000 1.3 abs \
--cwp 0.05 \
--2spaces \
--bg 35

---

I am currently having issues with Step 4; it has been over an hour, and it 
seems that the command will not finish executing. It is also not outputting any 
error messages. Whenever I run this analysis using the same parameters but 
without regressing out thickness, this step takes under five minutes on my 
machine and returns appropriate results. It seems like I must be doing 
something wrong, but I'm not sure. Please let me know if there is anything that 
you would change/add above.

Also, I noticed that you recommended regressing out the overall mean thickness 
(which you can obtain through mri_glmfit --surf fsaverage lh --osgm --y 
lh.thickness.fwhm10.mgh --o glm.osgm.lh --eres-save). Is glm.osgm.lh the mean 
stratified by class or the overall mean? If I were to include this in my GLM 
fit, would this be the correct command:

mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr lh.thickness.fwhm10.mgh glm.osgm.lh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

Thank you for taking a look at this, let me know if you need any other 
information.

Best,
Asim Dhungana

​Freesurfer version: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b



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Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

[Douglas N. Greve]

can you send your fsgd file and the Xg.dat file?

On 2/14/2022 1:21 AM, 정현우 wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to compare cortical surface area among three groups 
while controlling for estimated total intracranial volume (eTIV), as 
described on the Surface Based Group Analysis tutorial (*MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0 
). 



I ran the following command:

mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd 
three_group_comparison.area.fsgd dods --C 
three_group_comparison.area.mtx --surf fsaverage lh --cortex --glmdir 
three_group_comparison.area.lh.glmdir --eres-save


Then I got the following error:

gdfRead(): reading three_group_comparison.area.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 eTIV 1.53351e+06 139455
Class Size and Means of each Continuous Variable
1 0 42 1566070.5417
2 1 34 1515147.1360
3 2 15 1483959.5000
INFO: gd2mtx_method is dods
Reading source surface 
/media/sjkim/hd2/subject_data/fsaverage/surf/lh.white

Number of vertices 163842
Number of faces    327680
Total area         65417.00
AvgVtxArea       0.399269
AvgVtxDist       0.721953
StdVtxDist       0.195472

7.2.0
cwd /media/sjkim/hd2/subject_data/glm
cmdline mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd 
three_group_comparison.area.fsgd dods --C 
three_group_comparison.area.mtx --surf fsaverage lh --cortex --glmdir 
three_group_comparison.area.lh.glmdir --eres-save

sysname  Linux
hostname sjkim-System-Product-Name
machine  x86_64
user     sjkim
FixVertexAreaFlag = 1
UseMaskWithSmoothing     1
OneSampleGroupMean 0
y  /media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh
logyflag 0
usedti  0
FSGD three_group_comparison.area.fsgd
labelmask  /media/sjkim/hd2/subject_data/fsaverage/label/lh.cortex.label
maskinv 0
glmdir three_group_comparison.area.lh.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory three_group_comparison.area.lh.glmdir
Loading y from 
/media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh

   ... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to three_group_comparison.area.lh.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 833.575
Matrix condition is 1e+08
Found 149955 points in label.
Pruning voxels by thr: 1.175494e-38
Found 149953 voxels in mask
Saving mask to three_group_comparison.area.lh.glmdir/mask.mgh
Reshaping mriglm->mask...
search space = 74612.059149
DOF = 85
Starting fit and test
Fit completed in 0.0373833 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.997826, ar1std=0.000886, gstd=8.674183, fwhm=20.426140
Writing results
  three_group_comparison.area
    maxvox sig=3.0263  F=7.57212  at  index 107440 0 0  seed=1645215319
error: No such file or directory
error: MatrixMultiplyD(): m2 is null
 break 
/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596


I used FreeSurfer version 7.2.0 and Ubuntu 20.04.

I've searched the mail archives and similar errors have been reported 
in qdec, but I could not find any specific solution for this problem. 
Do you have any suggestions to solve this problem?


Thank you in advance,

Hyunwoo Jeong

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

[정현우]

External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to compare cortical surface area among three groups while
controlling for estimated total intracranial volume (eTIV), as described on
the Surface Based Group Analysis tutorial (
https://secure-web.cisco.com/1A0QSPCwnovVVVsFNKDP8OXxiBFqZ78jELzRvCgQt7us3rKayy2caTMVKC0nI4ildx0WJqzN5lLz1i-T5FHTbnyaiJAYj3f4mSQ4YHgEnKgBthfsubdAmofQmb_wxbJARZK70-yJh-Q-zB-SO-qUOdB5mSbQ71p0R-muUphnBpsvIZSn12rCp8u9iFutHnHZiR2SHvMYZrtWgA2qG1HwIVF7eXEz_S43Y9x_BasmQivW7O0E14rKYKn2Hc6i1PPi-krEJ-p90KuI4uEnOqU2T3HEQaZ4yicZdxZVpeFkSkL2Taw7LCrmTuBUijdwzR0I8MhzyhVIWFnyo-WUBgBXiig/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FGroupAnalysisV6.0

I ran the following command:

mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd
three_group_comparison.area.fsgd dods --C three_group_comparison.area.mtx
--surf fsaverage lh --cortex --glmdir three_group_comparison.area.lh.glmdir
--eres-save

Then I got the following error:

gdfRead(): reading three_group_comparison.area.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 eTIV 1.53351e+06 139455
Class Size and Means of each Continuous Variable
1 0 42 1566070.5417
2 1 34 1515147.1360
3 2 15 1483959.5000
INFO: gd2mtx_method is dods
Reading source surface /media/sjkim/hd2/subject_data/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 65417.00
AvgVtxArea   0.399269
AvgVtxDist   0.721953
StdVtxDist   0.195472

7.2.0
cwd /media/sjkim/hd2/subject_data/glm
cmdline mri_glmfit --y three_group_comparison.area.lh.10.mgh --fsgd
three_group_comparison.area.fsgd dods --C three_group_comparison.area.mtx
--surf fsaverage lh --cortex --glmdir three_group_comparison.area.lh.glmdir
--eres-save
sysname  Linux
hostname sjkim-System-Product-Name
machine  x86_64
user sjkim
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh
logyflag 0
usedti  0
FSGD three_group_comparison.area.fsgd
labelmask  /media/sjkim/hd2/subject_data/fsaverage/label/lh.cortex.label
maskinv 0
glmdir three_group_comparison.area.lh.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory three_group_comparison.area.lh.glmdir
Loading y from
/media/sjkim/hd2/subject_data/glm/three_group_comparison.area.lh.10.mgh
   ... done reading.
INFO: gd2mtx_method is dods
Saving design matrix to three_group_comparison.area.lh.glmdir/Xg.dat
Computing normalized matrix
Normalized matrix condition is 833.575
Matrix condition is 1e+08
Found 149955 points in label.
Pruning voxels by thr: 1.175494e-38
Found 149953 voxels in mask
Saving mask to three_group_comparison.area.lh.glmdir/mask.mgh
Reshaping mriglm->mask...
search space = 74612.059149
DOF = 85
Starting fit and test
Fit completed in 0.0373833 minutes
Computing spatial AR1 on surface
Residual: ar1mn=0.997826, ar1std=0.000886, gstd=8.674183, fwhm=20.426140
Writing results
  three_group_comparison.area
maxvox sig=3.0263  F=7.57212  at  index 107440 0 0seed=1645215319
error: No such file or directory
error: MatrixMultiplyD(): m2 is null
 break
/home/rd521/space_freesurfer/build/docker_ubuntu18/trunk/rd521-7.2.0/utils/matrix.cpp:596

I used FreeSurfer version 7.2.0 and Ubuntu 20.04.

I've searched the mail archives and similar errors have been reported in
qdec, but I could not find any specific solution for this problem. Do you
have any suggestions to solve this problem?

Thank you in advance,

Hyunwoo Jeong
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_glmfit of surface CBF maps while regressing out cortical thickness

[Douglas N. Greve]

Re: long run  time. Sorry, permutation will not work with PVR.
Re: mean thickness. Use the eres.mgh from you osgm analysis instead of 
the raw thickness map (lh.thickness.fwhm10.mgh)


On 2/8/2022 4:12 PM, Dhungana, Asim wrote:

Dear Freesurfer experts,

I am trying to run a GLM analysis comparing the difference in the 
cortical CBF maps between two groups, but I would like to regress out 
cortical thickness. I read through a post with a similar question 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65059.html), 
but I am still a little confused and want to confirm the steps of my 
analysis below:


---

1. Compile/smooth CBF data on surface for all subjects.
mris_preproc
--hemi lh \
--projfrac 0.5 \
--target fsaverage \
--o lh.cbf.00.mgh \
--iv subj1/cbf.mgz  subj1/register_pasl.dat \
--iv subj2/cbf.mgz  subj2/register_pasl.dat \
... until subjN

mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.cbf.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.cbf.fwhm10.mgh

2. Compile/smooth thickness data on surface for all subjects.
mris_preproc \
--fsgd cbf.fsgd \
--target fsaverage \
--hemi lh \
--meas thickness \
--out lh.thickness.00.mgh

mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.thickness.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.thickness.fwhm10.mgh

3. GLM fit of CBF maps, including thickness as a regressor.
mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr lh.thickness.fwhm10.mgh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

4. Multiple comparisons correction
mri_glmfit-sim \
--glmdir lh.cbf.fwhm10.glmdir \
--perm 1000 1.3 abs \
--cwp 0.05 \
--2spaces \
--bg 35

---

I am currently having issues with Step 4; it has been over an hour, 
and it seems that the command will not finish executing. It is also 
not outputting any error messages. Whenever I run this analysis using 
the same parameters but without regressing out thickness, this step 
takes under five minutes on my machine and returns appropriate 
results. It seems like I must be doing something wrong, but I'm not 
sure. Please let me know if there is anything that you would 
change/add above.


Also, I noticed that you recommended regressing out the overall mean 
thickness (which you can obtain through mri_glmfit --surf fsaverage lh 
--osgm --y lh.thickness.fwhm10.mgh --o glm.osgm.lh --eres-save). Is 
glm.osgm.lh the mean stratified by class or the overall mean? If I 
were to include this in my GLM fit, would this be the correct command:


mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr lh.thickness.fwhm10.mgh glm.osgm.lh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

Thank you for taking a look at this, let me know if you need any other 
information.


Best,
Asim Dhungana

​Freesurfer version: 
freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b


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[Freesurfer] mri_glmfit of surface CBF maps while regressing out cortical thickness

[Dhungana, Asim]

Dear Freesurfer experts,

I am trying to run a GLM analysis comparing the difference in the cortical CBF 
maps between two groups, but I would like to regress out cortical thickness. I 
read through a post with a similar question 
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65059.html), 
but I am still a little confused and want to confirm the steps of my analysis 
below:

---

1. Compile/smooth CBF data on surface for all subjects.
mris_preproc
--hemi lh \
--projfrac 0.5 \
--target fsaverage \
--o lh.cbf.00.mgh \
--iv subj1/cbf.mgz  subj1/register_pasl.dat \
--iv subj2/cbf.mgz  subj2/register_pasl.dat \
... until subjN

mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.cbf.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.cbf.fwhm10.mgh

2. Compile/smooth thickness data on surface for all subjects.
mris_preproc \
--fsgd cbf.fsgd \
--target fsaverage \
--hemi lh \
--meas thickness \
--out lh.thickness.00.mgh

mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.thickness.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.thickness.fwhm10.mgh

3. GLM fit of CBF maps, including thickness as a regressor.
mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr lh.thickness.fwhm10.mgh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

4. Multiple comparisons correction
mri_glmfit-sim \
--glmdir lh.cbf.fwhm10.glmdir \
--perm 1000 1.3 abs \
--cwp 0.05 \
--2spaces \
--bg 35

---

I am currently having issues with Step 4; it has been over an hour, and it 
seems that the command will not finish executing. It is also not outputting any 
error messages. Whenever I run this analysis using the same parameters but 
without regressing out thickness, this step takes under five minutes on my 
machine and returns appropriate results. It seems like I must be doing 
something wrong, but I'm not sure. Please let me know if there is anything that 
you would change/add above.

Also, I noticed that you recommended regressing out the overall mean thickness 
(which you can obtain through mri_glmfit --surf fsaverage lh --osgm --y 
lh.thickness.fwhm10.mgh --o glm.osgm.lh --eres-save). Is glm.osgm.lh the mean 
stratified by class or the overall mean? If I were to include this in my GLM 
fit, would this be the correct command:

mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr lh.thickness.fwhm10.mgh glm.osgm.lh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save

Thank you for taking a look at this, let me know if you need any other 
information.

Best,
Asim Dhungana

​Freesurfer version: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
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Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

[Tarumi Takashi]

External Email - Use Caution

Dear Dr. Yendiki,

Thank you so much for this additional explanation. It’s clear now.

Best regards,
Taka

> 2022/01/21 2:13、Yendiki, Anastasia のメール:
> 
> 
> Yes, the tutorial was written when the 7.2 release was in the last stages of 
> development. What happened between then and the final, released 7.2 was that 
> it now just figures out that the input is 1D by checking the dimensions of 
> the input, so you don't have to specify it on the command line.
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Tarumi Takashi 
> 
> Sent: Thursday, January 20, 2022 7:59 AM
> To: Freesurfer support list 
> Subject: Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized
>  
> External Email - Use Caution
> 
> Dear Dr. Yendiki,
> 
> Thank you so much for your reply. Yes, the command can run without the "--1d" 
> flag. But, I thought that the flag is "required for any along-tract analysis" 
> as stated in your TraculaStatistics instruction and highlighted in the 
> release notes for v7.2 (added 1D capability for mri_glmfit-sim). I would 
> greatly appreciate for your further clarifications. Thank you so much for 
> your help.
> 
> Best regards,
> Taka
> 
> On Thu, Jan 20, 2022 at 1:09 PM Yendiki, Anastasia  
> wrote:
> Hi Taka - Does it work when you remove the "--1d" from the command line? I 
> think that must be an error in the documentation.
> 
> Anastasia.
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Tarumi Takashi 
> 
> Sent: Wednesday, January 12, 2022 7:04 PM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized
>  
> External Email - Use Caution
> 
> Dear FreeSurfer Developers:
> 
> I am attempting to perform cluster-wise correction for the along-tract 
> measures, as described on the Tract statistics tutorial (MailScanner has 
> detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 
> https://secure-web.cisco.com/1MfvOB_RivuZacGakSlQntFiJmL3ek2B3qow_L8RuzHu3IW5D2fREF-sQi1qv3m9fC5W8DqHpEr5GP3uI86jIs2FGSd2j6oZRwohX-JENNPLRPc1VueNVOsfVQ-Zy9tMJj23fNN-DUylXWCYZAJaiLvJbv6rizKfL45IJHJmwMXF2rcaRSytczC1HEMx-iBASyUjg4tmaD1b3MkLdCNNjyoJzAT7YEsXcT29Xs3Y5St9-dVPp0Q7Efrl2W05gAQsXxeECJ0y-XlTJctTicvJTzQcUtrp_uchiT7Ejjv0qInvQQYLfdtEqXyzQoo7C6ieDj6X2RTmEIfP0Ig28orvLuA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTraculaStatistics
>  But, when I run the command below, the flag --1d is not recognized.
> 
> Command: mri_glmfit-sim --glmdir cc.bodyp.FA_Avg.glmdir --1d --cwp .05 --perm 
> 1000 1.3 pos
> Error: Flag --1d unrecognized.
> 
> I could not find similar errors reported. Does anyone have any thoughts on 
> how to trouble-shoot this? The FreeSurfer version I'm using is 7.2.0 on an M1 
> Mac machine with macOS 12.1. Thank you so much for your help.
> 
> Sincerely,
> Taka
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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> to continue communication over unencrypted e-mail, please notify the sender 
> of this message immed

Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

[Yendiki, Anastasia]

Yes, the tutorial was written when the 7.2 release was in the last stages of 
development. What happened between then and the final, released 7.2 was that it 
now just figures out that the input is 1D by checking the dimensions of the 
input, so you don't have to specify it on the command line.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Tarumi Takashi 

Sent: Thursday, January 20, 2022 7:59 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized


External Email - Use Caution

Dear Dr. Yendiki,

Thank you so much for your reply. Yes, the command can run without the "--1d" 
flag. But, I thought that the flag is "required for any along-tract analysis" 
as stated in your TraculaStatistics instruction and highlighted in the release 
notes for v7.2 (added 1D capability for mri_glmfit-sim). I would greatly 
appreciate for your further clarifications. Thank you so much for your help.

Best regards,
Taka

On Thu, Jan 20, 2022 at 1:09 PM Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Taka - Does it work when you remove the "--1d" from the command line? I 
think that must be an error in the documentation.

Anastasia.

From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Tarumi Takashi mailto:tak...@gmail.com>>
Sent: Wednesday, January 12, 2022 7:04 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized


External Email - Use Caution

Dear FreeSurfer Developers:

I am attempting to perform cluster-wise correction for the along-tract 
measures, as described on the Tract statistics tutorial (MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics<https://secure-web.cisco.com/1k_UHTgDkMyztiBV5VO6PazEUkIHIp4tFCos8o1vMfT5XasrL80AhnLun3nO3SbemuhiScR_HhzrdGaw0p1j5nK5lhe10k7-lPaCijiC0Vh7MQ0yuekVDkLDVrJqmG8Iv7dJngPrQuEM0Hi8ZnXXatPZFWA1aWQoWHkUSICt5kTu0nJuvpZHOUVg_RNMdlWUhH2kGUUGxeihwX0Nt22xOH5wPY2jNspczuzK2y2bSu-wVlXPvrnE1NXoh1Xk07_LOqY3hqWmAMeIEzH8SYeketuWolK-kKBMySEzU8Qcf85MkxF8ulxY7sh4wOn1doxI61CJ2S55Gnkqug92Kav4Oew/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTraculaStatistics>).
 But, when I run the command below, the flag --1d is not recognized.

Command: mri_glmfit-sim --glmdir cc.bodyp.FA_Avg.glmdir --1d --cwp .05 --perm 
1000 1.3 pos
Error: Flag --1d unrecognized.

I could not find similar errors reported. Does anyone have any thoughts on how 
to trouble-shoot this? The FreeSurfer version I'm using is 7.2.0 on an M1 Mac 
machine with macOS 12.1. Thank you so much for your help.

Sincerely,
Taka
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Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

[Tarumi Takashi]

External Email - Use Caution

Dear Dr. Yendiki,

Thank you so much for your reply. Yes, the command can run without the
"--1d" flag. But, I thought that the flag is "required for any along-tract
analysis" as stated in your TraculaStatistics instruction and highlighted
in the release notes for v7.2 (added 1D capability for mri_glmfit-sim). I
would greatly appreciate for your further clarifications. Thank you so much
for your help.

Best regards,
Taka

On Thu, Jan 20, 2022 at 1:09 PM Yendiki, Anastasia 
wrote:

> Hi Taka - Does it work when you remove the "--1d" from the command line? I
> think that must be an error in the documentation.
>
> Anastasia.
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Tarumi Takashi <
> tak...@gmail.com>
> *Sent:* Wednesday, January 12, 2022 7:04 PM
> *To:* freesurfer@nmr.mgh.harvard.edu 
> *Subject:* [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized
>
>
> External Email - Use Caution
>
> Dear FreeSurfer Developers:
>
> I am attempting to perform cluster-wise correction for the along-tract
> measures, as described on the Tract statistics tutorial (*MailScanner has
> detected a possible fraud attempt from "secure-web.cisco.com" claiming to
> be* 
> https://secure-web.cisco.com/14xTl-nXfhrT5s1HVQuP9A9vkMOy3hcNKfB2a4mLefQS6dl6-aqoECeHaosa2LFWdLTjGO9Fy1kpdjM631BpxovShFWZZnQP-Dhdr006lWhdN-X6ybWNDqx6uSWRU5YWSDVYXJgieK0q39yS1emZyDSqxj6jNaEcWN-5cwAEmoIVCE7D3-RJanSNI6Y0iBm7_FJQA64D0dGcvdndr0MX26xv_TB1PK0yL_ZbmoLx7M03L4-QTP3ky_P2xLnlWnkIdLXLbDrDPUsHQCR_om50OzamOsL2Xoz19qWPFmM38lhRQh0eJesWJzbQwhwh0WQyEAY2SL9gQ06L1NaykAWbh0Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTraculaStatistics
> <https://secure-web.cisco.com/1k_UHTgDkMyztiBV5VO6PazEUkIHIp4tFCos8o1vMfT5XasrL80AhnLun3nO3SbemuhiScR_HhzrdGaw0p1j5nK5lhe10k7-lPaCijiC0Vh7MQ0yuekVDkLDVrJqmG8Iv7dJngPrQuEM0Hi8ZnXXatPZFWA1aWQoWHkUSICt5kTu0nJuvpZHOUVg_RNMdlWUhH2kGUUGxeihwX0Nt22xOH5wPY2jNspczuzK2y2bSu-wVlXPvrnE1NXoh1Xk07_LOqY3hqWmAMeIEzH8SYeketuWolK-kKBMySEzU8Qcf85MkxF8ulxY7sh4wOn1doxI61CJ2S55Gnkqug92Kav4Oew/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTraculaStatistics>).
> But, when I run the command below, the flag --1d is not recognized.
>
> Command: mri_glmfit-sim --glmdir cc.bodyp.FA_Avg.glmdir --1d --cwp .05
> --perm 1000 1.3 pos
> Error: Flag --1d unrecognized.
>
> I could not find similar errors reported. Does anyone have any thoughts on
> how to trouble-shoot this? The FreeSurfer version I'm using is 7.2.0 on an
> M1 Mac machine with macOS 12.1. Thank you so much for your help.
>
> Sincerely,
> Taka
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

[Yendiki, Anastasia]

Hi Taka - Does it work when you remove the "--1d" from the command line? I 
think that must be an error in the documentation.

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Tarumi Takashi 

Sent: Wednesday, January 12, 2022 7:04 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized


External Email - Use Caution

Dear FreeSurfer Developers:

I am attempting to perform cluster-wise correction for the along-tract 
measures, as described on the Tract statistics tutorial (MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TraculaStatistics<https://secure-web.cisco.com/1k_UHTgDkMyztiBV5VO6PazEUkIHIp4tFCos8o1vMfT5XasrL80AhnLun3nO3SbemuhiScR_HhzrdGaw0p1j5nK5lhe10k7-lPaCijiC0Vh7MQ0yuekVDkLDVrJqmG8Iv7dJngPrQuEM0Hi8ZnXXatPZFWA1aWQoWHkUSICt5kTu0nJuvpZHOUVg_RNMdlWUhH2kGUUGxeihwX0Nt22xOH5wPY2jNspczuzK2y2bSu-wVlXPvrnE1NXoh1Xk07_LOqY3hqWmAMeIEzH8SYeketuWolK-kKBMySEzU8Qcf85MkxF8ulxY7sh4wOn1doxI61CJ2S55Gnkqug92Kav4Oew/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTraculaStatistics>).
 But, when I run the command below, the flag --1d is not recognized.

Command: mri_glmfit-sim --glmdir cc.bodyp.FA_Avg.glmdir --1d --cwp .05 --perm 
1000 1.3 pos
Error: Flag --1d unrecognized.

I could not find similar errors reported. Does anyone have any thoughts on how 
to trouble-shoot this? The FreeSurfer version I'm using is 7.2.0 on an M1 Mac 
machine with macOS 12.1. Thank you so much for your help.

Sincerely,
Taka
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[Freesurfer] mri_glmfit-sim error: Flag --1d unrecognized

[Tarumi Takashi]

External Email - Use Caution

Dear FreeSurfer Developers:

I am attempting to perform cluster-wise correction for the along-tract
measures, as described on the Tract statistics tutorial (
https://secure-web.cisco.com/1k_UHTgDkMyztiBV5VO6PazEUkIHIp4tFCos8o1vMfT5XasrL80AhnLun3nO3SbemuhiScR_HhzrdGaw0p1j5nK5lhe10k7-lPaCijiC0Vh7MQ0yuekVDkLDVrJqmG8Iv7dJngPrQuEM0Hi8ZnXXatPZFWA1aWQoWHkUSICt5kTu0nJuvpZHOUVg_RNMdlWUhH2kGUUGxeihwX0Nt22xOH5wPY2jNspczuzK2y2bSu-wVlXPvrnE1NXoh1Xk07_LOqY3hqWmAMeIEzH8SYeketuWolK-kKBMySEzU8Qcf85MkxF8ulxY7sh4wOn1doxI61CJ2S55Gnkqug92Kav4Oew/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTraculaStatistics
But, when I run the command below, the flag --1d is not recognized.

Command: mri_glmfit-sim --glmdir cc.bodyp.FA_Avg.glmdir --1d --cwp .05
--perm 1000 1.3 pos
Error: Flag --1d unrecognized.

I could not find similar errors reported. Does anyone have any thoughts on
how to trouble-shoot this? The FreeSurfer version I'm using is 7.2.0 on an
M1 Mac machine with macOS 12.1. Thank you so much for your help.

Sincerely,
Taka
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Re: [Freesurfer] mri_glmfit 0 voxels in mask ERROR

[Douglas N. Greve]

Do you see the note: "make sure at least one voxel has a non-zero value 
for each input"? To do this, you can try loading the input into 
freeview, eg,


tksurferfv fsaverage lh inflated -ov h.N0s2_e4pos.10.mgh -fminmax .0001 1
It will come up with a map of the first subject. Scroll through the 
subjects using the "frame" button. Look for one or more subjects where 
the values are 0 across the surface



On 9/15/2021 4:50 PM, Tsiknia, Amaryllis wrote:


External Email - Use Caution

Sorry about that! Here's the full terminal output:

cwd /space/syn01/1/data/MMILDB/MCE_RBS/fsurf

cmdline mri_glmfit.bin --y lh.N0s2_e4pos.10.mgh --fsgd 
./fsgd_omega/e4_positive.fsgd dods --C ./mtx_omega/e4_positive.mtx 
--surf fsaverage lh --cortex --glmdir lh.N0s2_e4pos.glmdir


sysnameLinux

hostname ip27.ucsd.edu

machinex86_64

user mmilrec5

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y/space/syn01/1/data/MMILDB/MCE_RBS/fsurf/lh.N0s2_e4pos.10.mgh

logyflag 0

usedti0

FSGD ./fsgd_omega/e4_positive.fsgd

labelmask/usr/pubsw/packages/freesurfer/RH4-x86_64-R600/subjects/fsaverage/label/lh.cortex.label

maskinv 0

glmdir lh.N0s2_e4pos.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory lh.N0s2_e4pos.glmdir

Loading y from 
/space/syn01/1/data/MMILDB/MCE_RBS/fsurf/lh.N0s2_e4pos.10.mgh


... done reading.

INFO: gd2mtx_method is dods

Saving design matrix to lh.N0s2_e4pos.glmdir/Xg.dat

Computing normalized matrix

Normalized matrix condition is 13.691

Matrix condition is 98.2187

Found 149955 points in label.

Pruning voxels by thr: 1.175494e-38

Found 0 voxels in mask

ERROR: no voxels found in the mask

make sure at least one voxel has a non-zero value for each input



*From:* freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Sent:* Wednesday, September 15, 2021 1:19 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] mri_glmfit 0 voxels in mask ERROR
Can't see the image. Can you just cut-and-paste the full terminal 
output into the email?


On 9/15/2021 3:02 PM, Tsiknia, Amaryllis wrote:


External Email - Use Caution

Dear Freesurfer Team,

I have been struggling with an error using the mri_gmfit command. I 
have been trying to run a simple surface-based group analysis on 28 
subjects testing whether a continuous variable "OMEGA3_457" relates 
to various RSI measures while adjusting for the effects of gender.


This is the error I am getting:

Image preview

and attached is my .fsgd file. The matrix file I am using is testing 
for the following contrast: 0 0 0.5 0.5.


I produced the lh.N0s2_e4pos.10.mgh file using the mri_surf2surf 
command after using mri_concat to concatenate the RSI data for all 28 
of our subjects into a single lh.N0s2_e4pos.00.mgh file. I have also 
attached thetext file (containing all the paths to the subject data) 
that was fed into the mri_concat command.


Any help would be immensely appreciated.

Thank you,

Amaryllis A. Tsiknia
/Imaging Researcher/
Department of Neurosciences
University of California, San Diego
atsik...@health.ucsd.edu <mailto:atsik...@health.ucsd.edu>


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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] mri_glmfit 0 voxels in mask ERROR

[Tsiknia, Amaryllis]

External Email - Use Caution

Sorry about that! Here's the full terminal output:


cwd /space/syn01/1/data/MMILDB/MCE_RBS/fsurf

cmdline mri_glmfit.bin --y lh.N0s2_e4pos.10.mgh --fsgd 
./fsgd_omega/e4_positive.fsgd dods --C ./mtx_omega/e4_positive.mtx --surf 
fsaverage lh --cortex --glmdir lh.N0s2_e4pos.glmdir

sysname  Linux

hostname ip27.ucsd.edu

machine  x86_64

user mmilrec5

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y/space/syn01/1/data/MMILDB/MCE_RBS/fsurf/lh.N0s2_e4pos.10.mgh

logyflag 0

usedti  0

FSGD ./fsgd_omega/e4_positive.fsgd

labelmask  
/usr/pubsw/packages/freesurfer/RH4-x86_64-R600/subjects/fsaverage/label/lh.cortex.label

maskinv 0

glmdir lh.N0s2_e4pos.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory lh.N0s2_e4pos.glmdir

Loading y from /space/syn01/1/data/MMILDB/MCE_RBS/fsurf/lh.N0s2_e4pos.10.mgh

   ... done reading.

INFO: gd2mtx_method is dods

Saving design matrix to lh.N0s2_e4pos.glmdir/Xg.dat

Computing normalized matrix

Normalized matrix condition is 13.691

Matrix condition is 98.2187

Found 149955 points in label.

Pruning voxels by thr: 1.175494e-38

Found 0 voxels in mask

ERROR: no voxels found in the mask

  make sure at least one voxel has a non-zero value for each input


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Wednesday, September 15, 2021 1:19 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] mri_glmfit 0 voxels in mask ERROR

Can't see the image. Can you just cut-and-paste the full terminal output into 
the email?

On 9/15/2021 3:02 PM, Tsiknia, Amaryllis wrote:

External Email - Use Caution

Dear Freesurfer Team,

I have been struggling with an error using the mri_gmfit command. I have been 
trying to run a simple surface-based group analysis on 28 subjects testing 
whether a continuous variable "OMEGA3_457" relates to various RSI measures 
while adjusting for the effects of gender.

This is the error I am getting:

[Image preview]

and attached is my .fsgd file. The matrix file I am using is testing for the 
following contrast: 0 0 0.5 0.5.

I produced the lh.N0s2_e4pos.10.mgh file using the mri_surf2surf command after 
using mri_concat to concatenate the RSI data for all 28 of our subjects into a 
single lh.N0s2_e4pos.00.mgh file. I have also attached the text file 
(containing all the paths to the subject data) that was fed into the mri_concat 
command.

Any help would be immensely appreciated.

Thank you,

Amaryllis A. Tsiknia
Imaging Researcher
Department of Neurosciences
University of California, San Diego
atsik...@health.ucsd.edu<mailto:atsik...@health.ucsd.edu>




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Re: [Freesurfer] mri_glmfit 0 voxels in mask ERROR

[Douglas N. Greve]

Can't see the image. Can you just cut-and-paste the full terminal output 
into the email?


On 9/15/2021 3:02 PM, Tsiknia, Amaryllis wrote:


External Email - Use Caution

Dear Freesurfer Team,

I have been struggling with an error using the mri_gmfit command. I 
have been trying to run a simple surface-based group analysis on 28 
subjects testing whether a continuous variable "OMEGA3_457" relates to 
various RSI measures while adjusting for the effects of gender.


This is the error I am getting:

Image preview

and attached is my .fsgd file. The matrix file I am using is testing 
for the following contrast: 0 0 0.5 0.5.


I produced the lh.N0s2_e4pos.10.mgh file using the mri_surf2surf 
command after using mri_concat to concatenate the RSI data for all 28 
of our subjects into a single lh.N0s2_e4pos.00.mgh file. I have also 
attached thetext file (containing all the paths to the subject data) 
that was fed into the mri_concat command.


Any help would be immensely appreciated.

Thank you,

Amaryllis A. Tsiknia
/Imaging Researcher/
Department of Neurosciences
University of California, San Diego
atsik...@health.ucsd.edu


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contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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continue to communicate over unencrypted e-mail. 

[Freesurfer] mri_glmfit 0 voxels in mask ERROR

[Tsiknia, Amaryllis]

External Email - Use Caution

Dear Freesurfer Team,

I have been struggling with an error using the mri_gmfit command. I have been 
trying to run a simple surface-based group analysis on 28 subjects testing 
whether a continuous variable "OMEGA3_457" relates to various RSI measures 
while adjusting for the effects of gender.

This is the error I am getting:

[Image preview]

and attached is my .fsgd file. The matrix file I am using is testing for the 
following contrast: 0 0 0.5 0.5.

I produced the lh.N0s2_e4pos.10.mgh file using the mri_surf2surf command after 
using mri_concat to concatenate the RSI data for all 28 of our subjects into a 
single lh.N0s2_e4pos.00.mgh file. I have also attached the text file 
(containing all the paths to the subject data) that was fed into the mri_concat 
command.

Any help would be immensely appreciated.

Thank you,

Amaryllis A. Tsiknia
Imaging Researcher
Department of Neurosciences
University of California, San Diego
atsik...@health.ucsd.edu

FSURF_RBS01LJ00504_20160108_110442_20160108.110442_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ01885_20140213_124057_20140213.124057_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ01985_20141114_121221_20141114.121221_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ02258_20150529_120557_20150529.120557_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ03293_20151118_120348_20151118.120348_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ03583_20160408_115730_20160408.115730_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ03738_20160617_114857_20160617.114857_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ03877_20150320_115330_20150320.115330_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ04458_20150204_113710_20150204.113710_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ04829_20160331_113751_20160331.113751_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ05281_20151022_102545_20151022.102545_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ05449_20160706_120010_20160706.120010_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ05501_20140423_115304_20140423.115304_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ05635_20140911_124649_20140911.124649_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ05748_20140312_124653_20140312.124653_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ05907_20150304_115018_20150304.115018_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ06270_20150121_121845_20150121.121845_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ06323_20140730_125445_20140730.125445_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ06331_20140903_125402_20140903.125402_1/surf/lh.N0s2.mgz
FSURF_RBSBDV100223_20150429_120910_20150429.120910_1/surf/lh.N0s2.mgz
FSURF_RBSV1LJ00557_20150424_121352_20150424.121352_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ00467_20150313_104521_20150313.104521_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ01871_20160224_115500_20160224.115500_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ02257_20140320_125048_20140320.125048_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ03085_20160113_115309_20160113.115309_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ04042_20140813_113552_20140813.113552_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ04220_20150114_110359_20150114.110359_1/surf/lh.N0s2.mgz
FSURF_RBS01LJ05610_20141107_114110_20141107.114110_1/surf/lh.N0s2.mgz



e4_positive.fsgd
Description: e4_positive.fsgd
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Re: [Freesurfer] mri_glmfit-sim error

[Douglas N. Greve]

This happens because the cached p-values were generated from a 
simulation that only went up to 30mm FWHM of smoothing. lGI has lots of 
internal smoothness which often pushes it over this level. You can try 
not using any smoothing, or, even better, try using permutation instead. 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm


On 8/3/2021 11:56 AM, Harriet Cornwell wrote:


External Email - Use Caution

External Email - Use Caution

Hi FreeSurfer team,

I am currently trying to run a correlational analysis in FreeSurfer. I 
am able to run the preproc and mri_glmfit commands successfully, but I 
am getting error messages when running mri_glmfit-sim for lGI, 
thickness and area. An example error message is: ERROR: cannot find 
/usr/local/freesurfer6/freesurfer//average/mult-comp-cor/fsaverage/rh/cortex/fwhm55/abs/th40/mc-z.csd. 
I have attached the full terminal output so that you can see the 
variations of this error message that I am getting. Are you able to 
advise what the issue might be and how I might go about fixing the 
issue? Just for reference, I am using a smoothing value of 10 for 
volume, area and thickness, and 5 for lGI. I would also be happy to 
share my design matrix and scripts if that would make the 
troubleshooting easier.


Thank you in advance for any help you can offer.

Best wishes,

*Harriet Cornwell*

PhD Student | Department of Psychology

University of Bath | 10 West 2.08


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Re: [Freesurfer] mri_glmfit DOSS

[Dr. Cornelius Kronlage]

External Email - Use Caution

Thank you for your reply! Using DOSS is precisely what I was trying to do, but 
mri_glmfit doesn't let me. I worked around by creating the design matrix in 
matlab and specify it to mri_glmfit directly, but I was wondering whether this 
might be bug in the parsing of the FSGD file. As a minimal example to 
reproduce, see the attached file. Trying to run mri_glmfit (doesn't even need 
more input specified), I get:

$ mri_glmfit --fsgd dosstest.fsgd doss
gdfRead(): reading dosstest.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 C 32. 8.50417
1 D 0.56 0.496904
2 E 5.4 3.49956
Class Size and Means of each Continuous Variable
1 A  1  50.   1.   4. 
2 B  8  29.8750   0.5000   5.6250 
ERROR: Class A has 1 members. With 3 variables and using DODS, you need at 
least 4 members


dosstest.fsgd:
GroupDescriptorFile 1
Title DOSSTest
DOSS
Class A
Class B
Variables C D E
Input SUBJECT1 A 50 1 4
Input SUBJECT2 B 30 0 12
Input SUBJECT3 B 29 0 5
Input SUBJECT4 B 31 1 3
Input SUBJECT5 B 20 1 4
Input SUBJECT6 B 42 1 6
Input SUBJECT7 B 33 0 11
Input SUBJECT8 B 30 0 1
Input SUBJECT9 B 24 1 3


Concerning demeaning: I am only going to use a contrast vector for differences 
in intercept between the groups [-1 1 0 0 0] and had the understanding that 
demeaning would't be necessary in this case. Am I mistaken or is there other 
reasons to do this especially for eTIV?

Thank you very much and
with best wishes,
Cornelius



> Date: Fri, 9 Jul 2021 14:05:31 -0400
> From: "Douglas N. Greve" 
> Subject: Re: [Freesurfer] mri_glmfit DOSS
> 
> You cannot use a DODS in this design as it tries to fit an offset and a 
> slope for each class, which can't be done when the class has only one 
> member. Try using DOSS instead. You should probably demean and rescale 
> the eTIV to be between 0 and 1.
> 
> On 6/29/2021 11:19 AM, Dr. Cornelius Kronlage wrote:
> >
> > External Email - Use Caution
> >
> > Dear freesurfers,
> >
> > for a morphometry study, I am comparing a single subject at a time to 
> > a group of controls. I would like to include age, gender (as a 
> > continuous variable for the sake of simplicity) and eTIV as ?nuisance? 
> > regressors in the GLM. The FSGD looks like this:
> >
> > GroupDescriptorFile 1
> > ?? ?Title SUBJECT1_vs_allControls
> > ?? ?Class Test
> > ?? ?Class Controls
> > ?? ?Variables Age Gender eTIV
> >
> > Input SUBJECT1 Test 50 1 1497422.2500
> > Input SUBJECT2 Controls 30 0 1709039.536815
> > Input SUBJECT3 Controls 29 0 1423097.816203
> > Input SUBJECT4 Controls 31 1 1524690.026713
> > ...
> >
> > When I try to run mri_glmfit I get the following error even though I 
> > specify DOSS:
> >
> > $ mri_glmfit --fsgd SUBJECT1_vs_allControls.fsgd doss [...]
> >
> > gdfRead(): reading SUBJECT1_vs_allControls.fsgd
> > WARNING: variable 1 is "Gender" which is often a discrete factor
> > ? The proper way to handle discrete factors is to create classes.
> > ? See 
> > https://secure-web.cisco.com/1pPOfqP7ALbHwAeCTJZowgLS8JJNUeA6-Z2RJlgx_6oCnQF0gABWOt_8KrLqoDdcjmbmoG9ym3ZtPvsAO1c68acEYJzrAsmFdzEWgPvb3kdwepaF35Hzwy4XTDhf8Mva0E4aHKtONsEKO44MeLe-FQDGn8hTUhVHWbd0M4oGtpgCfj_my9jlt9AoVNwgwNCyT4FImqIZy43WM2t69wzhU5ZyWyod4Pz_knEoEKB7FwqV3UX65_75Yv5PUJdpQmY_K9lKjYA0GH86Cv6X2Ru5JnQFHsGQgC0Rt3QRHIzfsrzg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
> > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> > Continuous Variable Means (all subjects)
> > 0 Age 28.6875 6.36611
> > 1 Gender 0.46875 0.499022
> > 2 eTIV 1.51444e+06 125811
> > Class Size and Means of each Continuous Variable
> > 1 Test? 1? 50.?? 1. 1497422.2500
> > 2 Controls 31? 28.?? 0.4516 1514993.8589
> > ERROR: Class Test has 1 members. With 3 variables and using DODS, you 
> > need at least 4 members
> >
> > How do I get mri_glmfit to use DOSS, or do I have to specify the 
> > design matrix by hand in this case?
> >
> > Thank you!
> >
> > Best wishes
> > Cornelius
> >
> >

dosstest.fsgd
Description: dosstest.fsgd
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Re: [Freesurfer] mri_glmfit DOSS

[Douglas N. Greve]

You cannot use a DODS in this design as it tries to fit an offset and a 
slope for each class, which can't be done when the class has only one 
member. Try using DOSS instead. You should probably demean and rescale 
the eTIV to be between 0 and 1.


On 6/29/2021 11:19 AM, Dr. Cornelius Kronlage wrote:


External Email - Use Caution

Dear freesurfers,

for a morphometry study, I am comparing a single subject at a time to 
a group of controls. I would like to include age, gender (as a 
continuous variable for the sake of simplicity) and eTIV as “nuisance” 
regressors in the GLM. The FSGD looks like this:


GroupDescriptorFile 1
    Title SUBJECT1_vs_allControls
    Class Test
    Class Controls
    Variables Age Gender eTIV

Input SUBJECT1 Test 50 1 1497422.2500
Input SUBJECT2 Controls 30 0 1709039.536815
Input SUBJECT3 Controls 29 0 1423097.816203
Input SUBJECT4 Controls 31 1 1524690.026713
...

When I try to run mri_glmfit I get the following error even though I 
specify DOSS:


$ mri_glmfit --fsgd SUBJECT1_vs_allControls.fsgd doss [...]

gdfRead(): reading SUBJECT1_vs_allControls.fsgd
WARNING: variable 1 is "Gender" which is often a discrete factor
  The proper way to handle discrete factors is to create classes.
  See https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 28.6875 6.36611
1 Gender 0.46875 0.499022
2 eTIV 1.51444e+06 125811
Class Size and Means of each Continuous Variable
1 Test  1  50.   1. 1497422.2500
2 Controls 31  28.   0.4516 1514993.8589
ERROR: Class Test has 1 members. With 3 variables and using DODS, you 
need at least 4 members


How do I get mri_glmfit to use DOSS, or do I have to specify the 
design matrix by hand in this case?


Thank you!

Best wishes
Cornelius


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Re: [Freesurfer] mri_glmfit DOSS

[Dr. Cornelius Kronlage]

External Email - Use Caution

Dear all,

this error seems to be gdfCheckNPerClass in utils/fsgdf.cpp. Using "doss" or 
"DOSS" as a tag in the FSGD file doesn't help either, strangely. Could it be 
that it should be strcasecmp() instead of strcmp() in line 1046 of fsgdf.cpp?

Cheers,
Cornelius


Date: Tue, 29 Jun 2021 15:19:20 +
From: "Dr. Cornelius Kronlage"
     
Subject: [Freesurfer] mri_glmfit DOSS
To: "'freesurfer@nmr.mgh.harvard.edu'"

Message-ID: <2a173629cd4540769ec6a07d892ca...@med.uni-tuebingen.de>
Content-Type: text/plain; charset="us-ascii"

External Email - Use Caution

Dear freesurfers,

for a morphometry study, I am comparing a single subject at a time to a group 
of controls. I would like to include age, gender (as a continuous variable for 
the sake of simplicity) and eTIV as "nuisance" regressors in the GLM. The FSGD 
looks like this:

GroupDescriptorFile 1
Title SUBJECT1_vs_allControls
Class Test
Class Controls
Variables Age Gender eTIV
Input SUBJECT1 Test 50 1 1497422.2500
Input SUBJECT2 Controls 30 0 1709039.536815
Input SUBJECT3 Controls 29 0 1423097.816203
Input SUBJECT4 Controls 31 1 1524690.026713
...



When I try to run mri_glmfit I get the following error even though I specify 
DOSS:



$ mri_glmfit --fsgd SUBJECT1_vs_allControls.fsgd doss [...]
gdfRead(): reading SUBJECT1_vs_allControls.fsgd
WARNING: variable 1 is "Gender" which is often a discrete factor
  The proper way to handle discrete factors is to create classes.
  See 
https://secure-web.cisco.com/10ThHTirv10OEqbkasMHR-FObJ8JCIIzwnlckPdClcabJkNNzasGdp_baoY3vFivUVTYKJkWgkuc4zGLEuruJqTFJupPLGS1I-n-IqrMT71wsYNjafciK0No5U2Ht7uG3R-qFReinEp_MecJ9YmfIFhW0ziWBvX_nknV20c9cIGk7hfeC2raoWWBVBbBw6-fQ_YasVd7Tv4WOYVgHcneMGz-jBtgcojHACBL4ql-DTGUQtWydFrpa2B2CXNbzOyFKzQJNEgklSCSyEgY8q0aHfg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 28.6875 6.36611
1 Gender 0.46875 0.499022
2 eTIV 1.51444e+06 125811
Class Size and Means of each Continuous Variable
1 Test  1  50.   1. 1497422.2500
2 Controls 31  28.   0.4516 1514993.8589
ERROR: Class Test has 1 members. With 3 variables and using DODS, you need at 
least 4 members
How do I get mri_glmfit to use DOSS, or do I have to specify the design matrix 
by hand in this case?

Thank you!
Best wishes
Cornelius



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[Freesurfer] mri_glmfit DOSS

[Dr. Cornelius Kronlage]

External Email - Use Caution

Dear freesurfers,



for a morphometry study, I am comparing a single subject at a time to a group 
of controls. I would like to include age, gender (as a continuous variable for 
the sake of simplicity) and eTIV as "nuisance" regressors in the GLM. The FSGD 
looks like this:


GroupDescriptorFile 1
Title SUBJECT1_vs_allControls
Class Test
Class Controls
Variables Age Gender eTIV
Input SUBJECT1 Test 50 1 1497422.2500
Input SUBJECT2 Controls 30 0 1709039.536815
Input SUBJECT3 Controls 29 0 1423097.816203
Input SUBJECT4 Controls 31 1 1524690.026713
...



When I try to run mri_glmfit I get the following error even though I specify 
DOSS:



$ mri_glmfit --fsgd SUBJECT1_vs_allControls.fsgd doss [...]
gdfRead(): reading SUBJECT1_vs_allControls.fsgd
WARNING: variable 1 is "Gender" which is often a discrete factor
  The proper way to handle discrete factors is to create classes.
  See 
https://secure-web.cisco.com/10ThHTirv10OEqbkasMHR-FObJ8JCIIzwnlckPdClcabJkNNzasGdp_baoY3vFivUVTYKJkWgkuc4zGLEuruJqTFJupPLGS1I-n-IqrMT71wsYNjafciK0No5U2Ht7uG3R-qFReinEp_MecJ9YmfIFhW0ziWBvX_nknV20c9cIGk7hfeC2raoWWBVBbBw6-fQ_YasVd7Tv4WOYVgHcneMGz-jBtgcojHACBL4ql-DTGUQtWydFrpa2B2CXNbzOyFKzQJNEgklSCSyEgY8q0aHfg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 28.6875 6.36611
1 Gender 0.46875 0.499022
2 eTIV 1.51444e+06 125811
Class Size and Means of each Continuous Variable
1 Test  1  50.   1. 1497422.2500
2 Controls 31  28.   0.4516 1514993.8589
ERROR: Class Test has 1 members. With 3 variables and using DODS, you need at 
least 4 members
How do I get mri_glmfit to use DOSS, or do I have to specify the design matrix 
by hand in this case?

Thank you!
Best wishes
Cornelius
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Re: [Freesurfer] mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)

[Douglas N. Greve]

Don't use --grf with surfaces

On 6/15/2021 7:24 PM, Paul, Jhelum wrote:


External Email - Use Caution

Hello,

I also have the same error. I have been looking into all the tutorials 
available for Freesurfer v7 and trying to search why,


mri_glmfit-sim   --glmdir lh.age_gender_volume.glmdir   --grf 2 abs   
--cwp  0.05 --2spaces


is not working and throwing an error showing the following in the 
screenshot:


Is it possible to clarify which tutorial to follow for grf or 
volume-based and surface-based group analysis in Freesurfer v7 and 
what all multiple comparisons corrections can be done for volume and 
surface analysis?


Any suggestion is appreciated.

Thank you.

Regards,

Jhelum Paul




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Re: [Freesurfer] mri_glmfit with pvr

[Douglas N. Greve]

You need to include elements for the PVR regressors in your contrast. I 
see that you only have four elements in the examples below and four 
classes, so you will need to add more


On 6/9/2021 10:38 AM, std...@virgilio.it wrote:


External Email - Use Caution

Thanks

If I have 4 groups

GroupDescriptorFile 1
Title XXX
Class G1
Class G2
Class G3
Class G4

Input subj1 G1

Input subj2 G3

Input subj3 G2

Input subj4 G2

Input subj5 G4




Are the contrasts below corrected?

G1_only_thick 1 0 0 0

G2_only_thick 1 0 0 0

G3_only_thick 1 0 0 0

G4_only_thick 1 0 0 0

G1+G2-G3+G4_thick 0.5 0.5 -0.5 -0.5

G3+G4+G2+G1_thick -0.5 -0.5 0.5 0.5

G1+G2+G3+G4_thick 0.25 0.25 0.25 0.25

Thanks

Stefano



Yes, you use a "per-vertex map" (--pvr option to mri_glmfit). See, 
example, this thread *MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be* 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg18790.html 
On 
6/3/2021 10:22 AM, std...@virgilio.it wrote:


External Email - Use Caution Hi, how can I perform vertex
by vertex (surface) analysis of covariance between functional
connectivity data (FS-FAST) and cortical thickness, regressing out
the effect of groups?My mean concern is how buid the fsgd file.
Stefano 

Great news, thank you, Doug! Best, aga On 8/3/11 5:02 PM, "Douglas N 
Greve"  wrote:


>Hi Aga, what you have done is correct, no need to include the pvr in the
>fsgd.
>doug
>
>Burzynska, Aga wrote:
>> Dear all,
>> I am trying to make group level analysis of functional data on the
>>surface and add per-vertex regressors (PVR, here: cortical thickness)
>>into the design. When I view the results I have the feeling that the PVR
>>is not really included in the model:
>>
>> I am using the command:
>> mri_glmfit --glmdir lh_output --y cope1_lh_4D.mgh --fsgd
>>Group1versusGroup2.fsgd  --pvr lh.thickness.10.mgh --C
>>Group1only_thickness.mat --C Group2only_thickness.mat --C
>>Group1minusGroup2_thickness.mat --C Group2minusGroup1_thickness.mat --C
>>Group1plusGroup2_thickness.mat
>>
>> where
>> cope1_lh_4D.mgh contains the concatenated sig.mgh images from the fixed
>>level analysis (combining the runs) for each participant
>> fsgd file contains:
>> GroupDescriptorFile 1
>> Title Group1versusGroup2
>> Class Group1 
>> Class Group2

>> Input 1109 Group1
>> Input 1110 Group1
>> Input  Group1
>> Input 1112 Group1
>> ...
>> Input 2280  Group2
>> Input 2282  Group2
>> Input 2283  Group2
>> Input 2284  Group2
>>
>> The PVR is a file containing thickness maps for each participant,
>>concatenated in the same order as for the functional data.
>>
>> So there are 2 main regressors (1 factor, 2 levels), but the contrast
>>files contain 3 regressors (the third one is the PVE), for instance:
>> Group1minusGroup2_thickness.mat contains  1 -1 0.
>>
>> Does it look correct?
>> Should the pvr regressor be included in the fsdg file? How can I do it?
>>
>> Thank you very much for your help,
>> Cheers,
>> Aga
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer  

>>
>>
>>   
>
>-- 
>Douglas N. Greve, Ph.D.

>MGH-NMR Center
>gr...@nmr.mgh.harvard.edu
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
>
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>is
>addressed. If you believe this e-mail was sent to you in error and the
>e-mail
>contains patient information, please contact the Partners Compliance
>HelpLine at
>*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
http://www.partners.org/complianceline  

[Freesurfer] mri_glmfit with pvr

[stdp82]

External Email - Use Caution

Thanks

If I have 4 groups

GroupDescriptorFile 1
Title XXX
Class G1
Class G2
Class G3
Class G4

Input subj1 G1

Input subj2 G3

Input subj3 G2

Input subj4 G2

Input subj5 G4





Are the contrasts below corrected?

G1_only_thick 1 0 0 0

G2_only_thick 1 0 0 0

G3_only_thick 1 0 0 0

G4_only_thick 1 0 0 0

G1+G2-G3+G4_thick 0.5 0.5 -0.5 -0.5

G3+G4+G2+G1_thick -0.5 -0.5 0.5 0.5

G1+G2+G3+G4_thick 0.25 0.25 0.25 0.25

Thanks

Stefano





Yes, you use a "per-vertex map" (--pvr option to mri_glmfit). See, example, 
this thread 
https://secure-web.cisco.com/1951sWOE8h4m5NbLCNqMyCAH8IOXE-lQF7pVtK2O9WlGr4lhC_ZayJW3oVHincxLs53lKvn0Z-ft-svmipnYED9p-xyQou2z1oP685gnJy3DM4X5tON-4zkvd1sP1xWnF1nZd9lZy-XdrKD8EufxxsG-gOreUvYzG0cA8pE1W8jkaYloEpe1annxnW8XXl-kmnIHZf1--oFrTvMN64dAA6I2FO5CoCq1z-DrzvgSl3fP4l15sZISoKwYj68dddQJm69YYEODA7eKQ5rzp3VtndQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg18790.htmlOn
 6/3/2021 10:22 AM, std...@virgilio.it mailto:std...@virgilio.it wrote:


> External Email - Use Caution Hi, how can I perform vertex by vertex (surface) 
> analysis of covariance between functional connectivity data (FS-FAST) and 
> cortical thickness, regressing out the effect of groups?My mean concern is 
> how buid the fsgd file. Stefano
> 
Great news, thank you, Doug! Best, aga On 8/3/11 5:02 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu wrote:


>Hi Aga, what you have done is correct, no need to include the pvr in the
>fsgd.
>doug
>
>Burzynska, Aga wrote:
>> Dear all,
>> I am trying to make group level analysis of functional data on the
>>surface and add per-vertex regressors (PVR, here: cortical thickness)
>>into the design. When I view the results I have the feeling that the PVR
>>is not really included in the model:
>>
>> I am using the command:
>> mri_glmfit --glmdir lh_output --y cope1_lh_4D.mgh --fsgd
>>Group1versusGroup2.fsgd  --pvr lh.thickness.10.mgh --C
>>Group1only_thickness.mat --C Group2only_thickness.mat --C
>>Group1minusGroup2_thickness.mat --C Group2minusGroup1_thickness.mat --C
>>Group1plusGroup2_thickness.mat
>>
>> where
>> cope1_lh_4D.mgh contains the concatenated sig.mgh images from the fixed
>>level analysis (combining the runs) for each participant
>> fsgd file contains:
>> GroupDescriptorFile 1
>> Title Group1versusGroup2
>> Class Group1 
>> Class Group2
>> Input 1109 Group1
>> Input 1110 Group1
>> Input  Group1
>> Input 1112 Group1
>> ...
>> Input 2280  Group2
>> Input 2282  Group2
>> Input 2283  Group2
>> Input 2284  Group2
>>
>> The PVR is a file containing thickness maps for each participant,
>>concatenated in the same order as for the functional data.
>>
>> So there are 2 main regressors (1 factor, 2 levels), but the contrast
>>files contain 3 regressors (the third one is the PVE), for instance:
>> Group1minusGroup2_thickness.mat contains  1 -1 0.
>>
>> Does it look correct?
>> Should the pvr regressor be included in the fsdg file? How can I do it?
>>
>> Thank you very much for your help,
>> Cheers,
>> Aga
>>
>> ___
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>MGH-NMR Center
gr...@nmr.mgh.harvard.edu">>gr...@nmr.mgh.harvard.edu
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[Freesurfer] mri_glmfit with pvr

[stdp82]

External Email - Use Caution

Thanks

If I have 4 groups

GroupDescriptorFile 1
Title XXX
Class G1
Class G2
Class G3
Class G4

Input subj1 G1

Input subj2 G3

Input subj3 G2

Input subj4 G2

Input subj5 G4




Are the contrasts below corrected?

G1_only_thick 1 0 0 0

G2_only_thick 1 0 0 0

G3_only_thick 1 0 0 0

G4_only_thick 1 0 0 0

G1+G2-G3+G4_thick 0.5 0.5 -0.5 -0.5

G3+G4+G2+G1_thick -0.5 -0.5 0.5 0.5

G1+G2+G3+G4_thick 0.25 0.25 0.25 0.25

Thanks

Stefano



Yes, you use a "per-vertex map" (--pvr option to mri_glmfit). See, example, 
this thread 
https://secure-web.cisco.com/1AQW2Zmfaui0gjHDqfC-62qKrikS49RYbR7pNeQeTr2onenw4VdfUzxAD-yIGZ-RWjvqJqELbkeBxh-eEoHsrsM5sjWYXowa55h5HmDwS2HP-LGyy4SFdxgEGV4R5lhBK0pMIf8VhbvlMkoZpaRCGO9sEsN89fc0rgzYL83HiJvCE6vviDul0-oFKliOXHXlXxdd6kqkmidKljGOb8tcDOZX_cjdrLsH7G0YoQYuiemfio9U_qVDhfkyDU2t5DWXRvlVbn_e9Nkc3DJ7h0XjhCA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg18790.htmlOn
 6/3/2021 10:22 AM, std...@virgilio.it wrote:

> External Email - Use Caution Hi, how can I perform vertex by vertex (surface) 
> analysis of covariance between functional connectivity data (FS-FAST) and 
> cortical thickness, regressing out the effect of groups?My mean concern is 
> how buid the fsgd file. Stefano
> 

Great news, thank you, Doug! Best, aga On 8/3/11 5:02 PM, "Douglas N Greve" 
 wrote:

>Hi Aga, what you have done is correct, no need to include the pvr in the
>fsgd.
>doug
>
>Burzynska, Aga wrote:
>> Dear all,
>> I am trying to make group level analysis of functional data on the
>>surface and add per-vertex regressors (PVR, here: cortical thickness)
>>into the design. When I view the results I have the feeling that the PVR
>>is not really included in the model:
>>
>> I am using the command:
>> mri_glmfit --glmdir lh_output --y cope1_lh_4D.mgh --fsgd
>>Group1versusGroup2.fsgd  --pvr lh.thickness.10.mgh --C
>>Group1only_thickness.mat --C Group2only_thickness.mat --C
>>Group1minusGroup2_thickness.mat --C Group2minusGroup1_thickness.mat --C
>>Group1plusGroup2_thickness.mat
>>
>> where
>> cope1_lh_4D.mgh contains the concatenated sig.mgh images from the fixed
>>level analysis (combining the runs) for each participant
>> fsgd file contains:
>> GroupDescriptorFile 1
>> Title Group1versusGroup2
>> Class Group1 
>> Class Group2
>> Input 1109 Group1
>> Input 1110 Group1
>> Input  Group1
>> Input 1112 Group1
>> ...
>> Input 2280  Group2
>> Input 2282  Group2
>> Input 2283  Group2
>> Input 2284  Group2
>>
>> The PVR is a file containing thickness maps for each participant,
>>concatenated in the same order as for the functional data.
>>
>> So there are 2 main regressors (1 factor, 2 levels), but the contrast
>>files contain 3 regressors (the third one is the PVE), for instance:
>> Group1minusGroup2_thickness.mat contains  1 -1 0.
>>
>> Does it look correct?
>> Should the pvr regressor be included in the fsdg file? How can I do it?
>>
>> Thank you very much for your help,
>> Cheers,
>> Aga
>>
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>>
>>
>>   
>
>-- 
>Douglas N. Greve, Ph.D.
>MGH-NMR Center
>gr...@nmr.mgh.harvard.edu
>Phone Number: 617-724-2358
>Fax: 617-726-7422
>
>Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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>The information in this e-mail is intended only for the person to whom it
>is
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>e-mail
>contains patient information, please contact the Partners Compliance
>HelpLine at
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Re: [Freesurfer] mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)

[Douglas N. Greve]

look at the tutorial

On 6/1/2021 12:00 AM, Diógenes Bispo wrote:


External Email - Use Caution

I would like to know what other modification I should make to my 
script to run --grf (volume analysis):


- mris_preproc ??
- mri_glmfit (--surf in white)
- mri_glmfit-sim ??

Thanks.

Diogenes Bispo
diogenesdi...@gmail.com 



Em sáb., 29 de mai. de 2021 às 03:14, Diógenes Bispo 
mailto:diogenesdi...@gmail.com>> escreveu:


Hi Freesurfer team.

I made the following command:

#!/bin/tcsh
setenv study $argv[1]
foreach hemi (lh rh)
  foreach smoothing (10)
    foreach meas (volume)
        mris_preproc --fsgd FSGD/{$study}.fsgd \
          --cache-in {$meas}.fwhm{$smoothing}.fsaverage \
          --target fsaverage \
          --hemi {$hemi} \
          --out {$hemi}.{$meas}.{$study}.{$smoothing}.mgh
    end
  end
end

#!/bin/tcsh
set study = $argv[1]
foreach hemi (lh rh)
  foreach smoothness (10)
    foreach meas (volume)
        mri_glmfit \
        --y {$hemi}.{$meas}.{$study}.{$smoothness}.mgh \
        --fsgd FSGD/{$study}.fsgd dods \
        --C Contrasts/Contrast-1_group.diff.mtx \
        --C Contrasts/Contrast-2_group-x-age.mtx \
        --C Contrasts/Contrast-3_group-x-icv.mtx \
        --C Contrasts/Contrast-4_group-x-age-x-icv.mtx \
        --C Contrasts/Contrast-5_GCCV.intercept.mtx \
        --C Contrasts/Contrast-6_GCCV.age.mtx \
        --surf fsaverage {$hemi}  \
        --cortex  \
        --glmdir {$hemi}.{$meas}.{$study}.{$smoothness}.glmdir \
        --eres-save
    end
  end
end

#!/bin/tcsh
setenv study $argv[1]
foreach meas (volume)
  foreach hemi (lh rh)
    foreach smoothness (10)
      foreach dir ({$hemi}.{$meas}.{$study}.{$smoothness}.glmdir)
          mri_glmfit-sim \
          --glmdir {$dir} \
          --grf 2.0 neg \
          --cwp 0.05  \
          --2spaces \
      end
    end
  end
end

I have the following error:
...

mri_surfcluster --in
rh.volume.covid.10.glmdir/Contrast-1_group.diff/sig.mgh --mask
rh.volume.covid.10.glmdir/mask.mgh --cwsig

rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.mgh
--sum

rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.summary
--ocn
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.masked.mgh
--no-fixmni --csd-out
rh.volume.covid.10.glmdir/csd/all.grf.th2.0.neg-Contrast-1_group.diff.csd
--fwhm 13.965488 --hemi rh --subject fsaverage --thmin 2.0 --sign
neg --oannot
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.annot
--bonferroni 2 --surf white

ERROR: need --csd with --csd-out


How should I proceed to solve this problem?

Thanks

Diógenes Bispo
diogenesdi...@gmail.com 


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Re: [Freesurfer] mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)

[Diógenes Bispo]

External Email - Use Caution

I would like to know what other modification I should make to my script to
run --grf (volume analysis):

- mris_preproc ??
- mri_glmfit (--surf in white)
- mri_glmfit-sim ??

Thanks.

Diogenes Bispo
diogenesdi...@gmail.com



Em sáb., 29 de mai. de 2021 às 03:14, Diógenes Bispo <
diogenesdi...@gmail.com> escreveu:

> Hi Freesurfer team.
>
> I made the following command:
>
> #!/bin/tcsh
> setenv study $argv[1]
> foreach hemi (lh rh)
>   foreach smoothing (10)
> foreach meas (volume)
> mris_preproc --fsgd FSGD/{$study}.fsgd \
>   --cache-in {$meas}.fwhm{$smoothing}.fsaverage \
>   --target fsaverage \
>   --hemi {$hemi} \
>   --out {$hemi}.{$meas}.{$study}.{$smoothing}.mgh
> end
>   end
> end
> 
> #!/bin/tcsh
> set study = $argv[1]
> foreach hemi (lh rh)
>   foreach smoothness (10)
> foreach meas (volume)
> mri_glmfit \
> --y {$hemi}.{$meas}.{$study}.{$smoothness}.mgh \
> --fsgd FSGD/{$study}.fsgd dods \
> --C Contrasts/Contrast-1_group.diff.mtx \
> --C Contrasts/Contrast-2_group-x-age.mtx \
> --C Contrasts/Contrast-3_group-x-icv.mtx \
> --C Contrasts/Contrast-4_group-x-age-x-icv.mtx \
> --C Contrasts/Contrast-5_GCCV.intercept.mtx \
> --C Contrasts/Contrast-6_GCCV.age.mtx \
> --surf fsaverage {$hemi}  \
> --cortex  \
> --glmdir {$hemi}.{$meas}.{$study}.{$smoothness}.glmdir \
> --eres-save
> end
>   end
> end
> 
> #!/bin/tcsh
> setenv study $argv[1]
> foreach meas (volume)
>   foreach hemi (lh rh)
> foreach smoothness (10)
>   foreach dir ({$hemi}.{$meas}.{$study}.{$smoothness}.glmdir)
>   mri_glmfit-sim \
>   --glmdir {$dir} \
>   --grf 2.0 neg \
>   --cwp 0.05  \
>   --2spaces \
>   end
> end
>   end
> end
>
> I have the following error:
> ...
>
> mri_surfcluster --in
> rh.volume.covid.10.glmdir/Contrast-1_group.diff/sig.mgh --mask
> rh.volume.covid.10.glmdir/mask.mgh --cwsig
> rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.mgh
> --sum
> rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.summary
> --ocn
> rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.mgh
> --annot aparc --cwpvalthresh 0.05 --o
> rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.masked.mgh
> --no-fixmni --csd-out
> rh.volume.covid.10.glmdir/csd/all.grf.th2.0.neg-Contrast-1_group.diff.csd
> --fwhm 13.965488 --hemi rh --subject fsaverage --thmin 2.0 --sign neg
> --oannot
> rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.annot
> --bonferroni 2 --surf white
>
> ERROR: need --csd with --csd-out
>
> How should I proceed to solve this problem?
>
> Thanks
>
> Diógenes Bispo
> diogenesdi...@gmail.com
>
>
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Re: [Freesurfer] mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)

[Douglas N. Greve]

You can't use the --grf option with surfaces

On 5/29/2021 2:14 AM, Diógenes Bispo wrote:


External Email - Use Caution

Hi Freesurfer team.

I made the following command:

#!/bin/tcsh
setenv study $argv[1]
foreach hemi (lh rh)
  foreach smoothing (10)
    foreach meas (volume)
        mris_preproc --fsgd FSGD/{$study}.fsgd \
          --cache-in {$meas}.fwhm{$smoothing}.fsaverage \
          --target fsaverage \
          --hemi {$hemi} \
          --out {$hemi}.{$meas}.{$study}.{$smoothing}.mgh
    end
  end
end

#!/bin/tcsh
set study = $argv[1]
foreach hemi (lh rh)
  foreach smoothness (10)
    foreach meas (volume)
        mri_glmfit \
        --y {$hemi}.{$meas}.{$study}.{$smoothness}.mgh \
        --fsgd FSGD/{$study}.fsgd dods \
        --C Contrasts/Contrast-1_group.diff.mtx \
        --C Contrasts/Contrast-2_group-x-age.mtx \
        --C Contrasts/Contrast-3_group-x-icv.mtx \
        --C Contrasts/Contrast-4_group-x-age-x-icv.mtx \
        --C Contrasts/Contrast-5_GCCV.intercept.mtx \
        --C Contrasts/Contrast-6_GCCV.age.mtx \
        --surf fsaverage {$hemi}  \
        --cortex  \
        --glmdir {$hemi}.{$meas}.{$study}.{$smoothness}.glmdir \
        --eres-save
    end
  end
end

#!/bin/tcsh
setenv study $argv[1]
foreach meas (volume)
  foreach hemi (lh rh)
    foreach smoothness (10)
      foreach dir ({$hemi}.{$meas}.{$study}.{$smoothness}.glmdir)
          mri_glmfit-sim \
          --glmdir {$dir} \
          --grf 2.0 neg \
          --cwp 0.05  \
          --2spaces \
      end
    end
  end
end

I have the following error:
...

mri_surfcluster --in 
rh.volume.covid.10.glmdir/Contrast-1_group.diff/sig.mgh --mask 
rh.volume.covid.10.glmdir/mask.mgh --cwsig 
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.mgh 
--sum 
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.summary 
--ocn 
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.mgh 
--annot aparc --cwpvalthresh 0.05 --o 
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.masked.mgh 
--no-fixmni --csd-out 
rh.volume.covid.10.glmdir/csd/all.grf.th2.0.neg-Contrast-1_group.diff.csd 
--fwhm 13.965488 --hemi rh --subject fsaverage --thmin 2.0 --sign neg 
--oannot 
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.annot 
--bonferroni 2 --surf white


ERROR: need --csd with --csd-out


How should I proceed to solve this problem?

Thanks

Diógenes Bispo
diogenesdi...@gmail.com 


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The information in this e-mail is intended only for the person to whom it is 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
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[Freesurfer] mri_glmfit-sim with grf (ERROR: need --csd with --csd-out)

[Diógenes Bispo]

External Email - Use Caution

Hi Freesurfer team.

I made the following command:

#!/bin/tcsh
setenv study $argv[1]
foreach hemi (lh rh)
  foreach smoothing (10)
foreach meas (volume)
mris_preproc --fsgd FSGD/{$study}.fsgd \
  --cache-in {$meas}.fwhm{$smoothing}.fsaverage \
  --target fsaverage \
  --hemi {$hemi} \
  --out {$hemi}.{$meas}.{$study}.{$smoothing}.mgh
end
  end
end

#!/bin/tcsh
set study = $argv[1]
foreach hemi (lh rh)
  foreach smoothness (10)
foreach meas (volume)
mri_glmfit \
--y {$hemi}.{$meas}.{$study}.{$smoothness}.mgh \
--fsgd FSGD/{$study}.fsgd dods \
--C Contrasts/Contrast-1_group.diff.mtx \
--C Contrasts/Contrast-2_group-x-age.mtx \
--C Contrasts/Contrast-3_group-x-icv.mtx \
--C Contrasts/Contrast-4_group-x-age-x-icv.mtx \
--C Contrasts/Contrast-5_GCCV.intercept.mtx \
--C Contrasts/Contrast-6_GCCV.age.mtx \
--surf fsaverage {$hemi}  \
--cortex  \
--glmdir {$hemi}.{$meas}.{$study}.{$smoothness}.glmdir \
--eres-save
end
  end
end

#!/bin/tcsh
setenv study $argv[1]
foreach meas (volume)
  foreach hemi (lh rh)
foreach smoothness (10)
  foreach dir ({$hemi}.{$meas}.{$study}.{$smoothness}.glmdir)
  mri_glmfit-sim \
  --glmdir {$dir} \
  --grf 2.0 neg \
  --cwp 0.05  \
  --2spaces \
  end
end
  end
end

I have the following error:
...

mri_surfcluster --in
rh.volume.covid.10.glmdir/Contrast-1_group.diff/sig.mgh --mask
rh.volume.covid.10.glmdir/mask.mgh --cwsig
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.mgh
--sum
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.cluster.summary
--ocn
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.masked.mgh
--no-fixmni --csd-out
rh.volume.covid.10.glmdir/csd/all.grf.th2.0.neg-Contrast-1_group.diff.csd
--fwhm 13.965488 --hemi rh --subject fsaverage --thmin 2.0 --sign neg
--oannot
rh.volume.covid.10.glmdir/Contrast-1_group.diff/grf.th2.0.neg.sig.ocn.annot
--bonferroni 2 --surf white

ERROR: need --csd with --csd-out

How should I proceed to solve this problem?

Thanks

Diógenes Bispo
diogenesdi...@gmail.com
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Re: [Freesurfer] mri_glmfit FIR model

[Douglas N. Greve]

Yes, exactly on both questions

On 4/22/2021 8:23 AM, Marilena Wilding wrote:


External Email - Use Caution

External Email - Use Caution

Dear Freesurfers,

I’m currently doing 2nd level analysis on a FIR model.

I first concatenated my data with this command:

isxconcat-sess -sf sessidlist -analysis FIR_group.lh -contrast 
global-v-local -no-hrf -hemi lh -o group_analysis


I got 29 timepoints and their corresponding 29 ces.nii and cesvar.nii 
files.


Then I ran glmfit (for each timepoint):

mri_glmfit \

--y ces.000.nii \

--wls cesvar.000.nii.gz \

--surface fsaverage lh \

--glmdir group_GLM_lh_000.wls \

--osgm \

--nii.gz

In my paradigm I’m showing a stimulus that can be seen in two ways. In 
my analysis I separate the runs, depending on what the participant 
indicated to have seen (1 or 2) and compute the contrast in activation 
between these two percepts. I was now wondering if the command above 
is correct with the ‘osgm’-flag? Since I’m only interested in the 
difference between the two conditions from the paradigm and not 
different groups of participants (e.g. patients vs. healthy people) I 
don’t have to specify a fsgd file, correct? And if I wanted to specify 
covariates I’d just make such a file but without groups and only 
variables?


Thank you very much for your help!

Best,

Mara


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[Freesurfer] mri_glmfit FIR model

[Marilena Wilding]

External Email - Use Caution

Dear Freesurfers,

I’m currently doing 2nd level analysis on a FIR model.
I first concatenated my data with this command:

isxconcat-sess -sf sessidlist -analysis FIR_group.lh -contrast global-v-local 
-no-hrf -hemi lh -o group_analysis

I got 29 timepoints and their corresponding 29 ces.nii and cesvar.nii files.

Then I ran glmfit (for each timepoint):

mri_glmfit \
--y ces.000.nii \
--wls cesvar.000.nii.gz \
--surface fsaverage lh \
--glmdir group_GLM_lh_000.wls \
--osgm \
--nii.gz

In my paradigm I’m showing a stimulus that can be seen in two ways. In my 
analysis I separate the runs, depending on what the participant indicated to 
have seen (1 or 2) and compute the contrast in activation between these two 
percepts. I was now wondering if the command above is correct with the 
‘osgm’-flag? Since I’m only interested in the difference between the two 
conditions from the paradigm and not different groups of participants (e.g. 
patients vs. healthy people) I don’t have to specify a fsgd file, correct? And 
if I wanted to specify covariates I’d just make such a file but without groups 
and only variables?

Thank you very much for your help!

Best,
Mara

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Re: [Freesurfer] mri_glmfit error

[Douglas N. Greve]

The format is not correct. It should be
Input SubjectID Class
You have SubjectID in there twice

On 4/1/2021 1:15 AM, Ishi Tandon AIB, Jaipur wrote:


External Email - Use Caution

Hello FS experts,

I attempted to execute  mri_glmfit on my structural data through the 
following command -


mri_glmfit --y final.lh.mTBI.volume.10.mgh --fsgd FSGD/mild.tbi.fsgd 
dods -C contrats/HC-mTBI.mtx --surf fsaverage --cortex --glmdir 
lh.volume.glmdir


But it gives me an error (attached below) indicating a formatting 
problem in my FSGD file (attached).
I have been trying to figure that out for a while. But I am unable to 
debug it.


Could someone please help me resolve it?
Thanks for your time.

/Regards,/
/Ishi Tandon/
/B.Tech + M.Tech - Cognitive Neuroscience/
/Amity University, Rajasthan/



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[Freesurfer] mri_glmfit error

[Ishi Tandon AIB, Jaipur]

External Email - Use Caution

Hello FS experts,

I attempted to execute  mri_glmfit on my structural data through the
following command -

mri_glmfit --y final.lh.mTBI.volume.10.mgh --fsgd FSGD/mild.tbi.fsgd dods
-C contrats/HC-mTBI.mtx --surf fsaverage --cortex --glmdir lh.volume.glmdir

But it gives me an error (attached below) indicating a formatting problem
in my FSGD file (attached).
I have been trying to figure that out for a while. But I am unable to debug
it.

Could someone please help me resolve it?
Thanks for your time.

*Regards,*
*Ishi Tandon*
*B.Tech + M.Tech - Cognitive Neuroscience*
*Amity University, Rajasthan*


mild.tbi.fsgd
Description: Binary data
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Re: [Freesurfer] mri_glmfit dependent variable

[Douglas N. Greve]

On 2/23/2021 11:37 PM, miracle ozzoude wrote:


External Email - Use Caution

Thanks Doug. I appreciate it. I have more questions.

1) Aren't both models answering the same question regardless of which 
side of the equation cortical thickness or syndromes is placed?
Similar questions, but the results will not be identical. Eg, if 
cognition and thickness are identical numbers, then you can't solve 
Model 1 but you can solve Model 2. I was thinking you wanted to use the 
thickness from the entire cortex to estimate syndromes.


2) Also, I noticed in the mri_glmfit --help, it said that forward 
model 2 is inverted to solve for the regressor of interest. Correct if 
I'm wrong, does it mean if my matrix is 0 0 0 1 where 1 represents 
neuropsych syndrome, it will solve for it?
Yes, it will. But you will need to create an "image" of your neuropsych 
scores so that they are in each voxel.


The forward model is given by:


y = W*X*B + n


where X is the Ns-by-Nb design matrix, y is the Ns-by-Nv input data

set, B is the Nb-by-Nv regression parameters, and n is noise. Ns is

the number of inputs, Nb is the number of regressors, and Nv is the

number of voxels/vertices (all cols/rows/slices). y may be surface

or volume data and may or may not have been spatially smoothed. W

is a diagonal weighing matrix.


During the estimation stage, the forward model is inverted to

solve for B:


B = inv(X'W'*W*X)*X'W'y


3) Lastly, how do I extract the beta-values after running 
mri_glmfit-sim without matlab?
do you want a single beta as an overlay? Then use mri_convert and 
specify the frame you want with --frame (starts at 0). If you want 
values, you can run mri_convert beta.mgz --ascii beta.ascii


Many thanks,
Paul

On Tue, Feb 23, 2021 at 12:37 AM miracle ozzoude > wrote:


Hello Experts,

I've a question about mri_glmfit. I want to investigate the
association between thickness and neuropsychiatric syndromes,
controlling for age and cognition. Which model below is mri_glmfit
performing?

Model 1
neuropsych syndromes ~ age + cognition + cortical thickness
or
Model 2
cortical thickness ~ age + cognition + neuropsych syndrome

Many thanks,
Paul


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Re: [Freesurfer] mri_glmfit dependent variable

[miracle ozzoude]

External Email - Use Caution

Thanks Doug. I appreciate it. I have more questions.

1) Aren't both models answering the same question regardless of which side
of the equation cortical thickness or syndromes is placed?

2) Also, I noticed in the mri_glmfit --help, it said that forward model 2
is inverted to solve for the regressor of interest. Correct if I'm wrong,
does it mean if my matrix is 0 0 0 1 where 1 represents neuropsych
syndrome, it will solve for it?

The forward model is given by:


y = W*X*B + n


where X is the Ns-by-Nb design matrix, y is the Ns-by-Nv input data

set, B is the Nb-by-Nv regression parameters, and n is noise. Ns is

the number of inputs, Nb is the number of regressors, and Nv is the

number of voxels/vertices (all cols/rows/slices). y may be surface

or volume data and may or may not have been spatially smoothed. W

is a diagonal weighing matrix.


During the estimation stage, the forward model is inverted to

solve for B:


B = inv(X'W'*W*X)*X'W'y


3) Lastly, how do I extract the beta-values after running mri_glmfit-sim
without matlab?

Many thanks,
Paul

On Tue, Feb 23, 2021 at 12:37 AM miracle ozzoude 
wrote:

> Hello Experts,
>
> I've a question about mri_glmfit. I want to investigate the association
> between thickness and neuropsychiatric syndromes, controlling for age and
> cognition. Which model below is mri_glmfit performing?
>
> Model 1
> neuropsych syndromes ~ age + cognition + cortical thickness
> or
> Model 2
> cortical thickness ~ age + cognition + neuropsych syndrome
>
> Many thanks,
> Paul
>
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Re: [Freesurfer] mri_glmfit dependent variable

[Douglas N. Greve]

Model 2 is the only one we have the ability to fit. Model 1 would need 
some kind of machine learning method


On 2/23/2021 12:37 AM, miracle ozzoude wrote:


External Email - Use Caution

Hello Experts,

I've a question about mri_glmfit. I want to investigate the 
association between thickness and neuropsychiatric syndromes, 
controlling for age and cognition. Which model below is mri_glmfit 
performing?


Model 1
neuropsych syndromes ~ age + cognition + cortical thickness
or
Model 2
cortical thickness ~ age + cognition + neuropsych syndrome

Many thanks,
Paul

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[Freesurfer] mri_glmfit dependent variable

[miracle ozzoude]

External Email - Use Caution

Hello Experts,

I've a question about mri_glmfit. I want to investigate the association
between thickness and neuropsychiatric syndromes, controlling for age and
cognition. Which model below is mri_glmfit performing?

Model 1
neuropsych syndromes ~ age + cognition + cortical thickness
or
Model 2
cortical thickness ~ age + cognition + neuropsych syndrome

Many thanks,
Paul
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Re: [Freesurfer] mri_glmfit-sim

[Douglas N. Greve]

That can happen because the null distribution of the cluster sizes 
change when you change the threshold. So at a threshold of 1.3, you 
might have a slightly larger cluster (which improves the cluster 
p-value), but you pay a penalty for lowering the threshold (which hurts 
the cluster p-value). In this case, the penalty is worse than the benefit.


On 1/25/2021 9:24 PM, Nasiriavanaki, Zahra wrote:
I just wanted to add that the attached maps in the previous email, was 
made by the tksurfer command below. I also added the mri_glmfit command.


mri_glmfit --y cespct.nii.gz --osgm --glmdir main.wls --nii.gz --mask 
../mask.nii.gz  --surface fsaverage ${space:(-2)} --cortex --fwhm 5 
--no-prune


tksurfer fsaverage lh inflated -ov cache.th13.abs.sig.masked.mgh 
-fminmax 1.3 7


I appreciate if you could let me know your comments.

Thanks a lot!

*Zahra (Mona) Nasiriavanaki, M.D.*
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Boston, MA, USA, 02129

On Jan 22, 2021, at 6:28 PM, Nasiriavanaki, Zahra 
> wrote:


Hi Freesurferers

I am running mri_glmfit-sim to do multiple comparison correction with 
the command below. It goes through without any error. However when I 
view the corrected maps in tksurfer, I see some clusters in corrected 
map with p=2 and p=3, but I don’t see them in corrected map with 
p=1.3 (images attached). The contrast of interest is the same between 
the maps. The viewing threshold is 1.3 in p=1.3 maps and is 2 and 3 
in the p=2 and p=3 maps respectively.

I’m confused.
Could you please comment on that?

mri_glmfit-sim --glmdir main.wls --cache 1.3 abs --3spaces
mri_glmfit-sim --glmdir main.wls --cache 2 abs —3spaces


Thanks a lot
Mona



*Zahra (Mona) Nasiriavanaki, M.D.*
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Boston, MA, USA, 02129




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Re: [Freesurfer] mri_glmfit-sim

[Nasiriavanaki, Zahra]

I just wanted to add that the attached maps in the previous email, was made by 
the tksurfer command below. I also added the mri_glmfit command.

mri_glmfit --y cespct.nii.gz --osgm --glmdir main.wls --nii.gz --mask 
../mask.nii.gz  --surface fsaverage ${space:(-2)} --cortex --fwhm 5 --no-prune

tksurfer fsaverage lh inflated -ov cache.th13.abs.sig.masked.mgh -fminmax 1.3 7

I appreciate if you could let me know your comments.

Thanks a lot!

Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Boston, MA, USA, 02129

On Jan 22, 2021, at 6:28 PM, Nasiriavanaki, Zahra 
mailto:znasiriavan...@mgh.harvard.edu>> wrote:

Hi Freesurferers

I am running mri_glmfit-sim to do multiple comparison correction with the 
command below. It goes through without any error. However when I view the 
corrected maps in tksurfer, I see some clusters in corrected map with p=2 and 
p=3, but I don’t see them in corrected map with p=1.3 (images attached). The 
contrast of interest is the same between the maps. The viewing threshold is 1.3 
in p=1.3 maps and is 2 and 3 in the p=2 and p=3 maps respectively.
I’m confused.
Could you please comment on that?

mri_glmfit-sim --glmdir main.wls --cache 1.3 abs --3spaces
mri_glmfit-sim --glmdir main.wls --cache 2 abs —3spaces


Thanks a lot
Mona



Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Boston, MA, USA, 02129


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Re: [Freesurfer] mri_glmfit-sim error with no csd files generated

[Na, Xiaoxu]

External Email - Use Caution

Thank you for your confirmation! I tried the -perm as well and this error 
wouldn't show after using the csd files generated from permutation.

However, I have one more question. Shall I use -perm first in order to use 
-cache? If this is the case, the pial_lgi features went through well using the 
permutation, but once I tried -cache afterward, it showed the error as below 
with fwhm larger than 30, is there something wrong with the design? I don't 
understand quite much how this fwhm became this large by the way.
Thank you so much!


cmdline mri_glmfit --y sAnalysis/rh.pial_lgi.g2v2DSleepiness.10.mgh --fsgd 
sAnalysis/g2v2DSleepiness.fsgd dods --C sAnalysis/g1g2.sleepscore.mtx --surf 
fsaverage rh --cortex --glmdir sAnalysis/rh.pial_lgi.g2v2DSleepiness.10.glmdir 
--eres-save
SURFACE: fsaverage rh
log file is 
sAnalysis/rh.pial_lgi.g2v2DSleepiness.10.glmdir/cache.mri_glmfit-sim.log

cd /home/xiaoxu/8YearOldNiiB1
/home/xiaoxu/freesurfer/bin/mri_glmfit-sim
--glmdir sAnalysis/rh.pial_lgi.g2v2DSleepiness.10.glmdir --cache 4 pos --cwp 
0.05 --2spaces

mri_glmfit-sim 7.1.0
Wed Jan 13 14:08:23 CST 2021
Linux xnVMUbuntu18 5.4.0-59-generic #65~18.04.1-Ubuntu SMP Mon Dec 14 15:59:40 
UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
xiaoxu
setenv SUBJECTS_DIR /home/xiaoxu/8YearOldNiiB1
FREESURFER_HOME /home/xiaoxu/freesurfer

Original mri_glmfit command line:
cmdline mri_glmfit --y sAnalysis/rh.pial_lgi.g2v2DSleepiness.10.mgh --fsgd 
sAnalysis/g2v2DSleepiness.fsgd dods --C sAnalysis/g1g2.sleepscore.mtx --surf 
fsaverage rh --cortex --glmdir sAnalysis/rh.pial_lgi.g2v2DSleepiness.10.glmdir 
--eres-save

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 36.436322
ERROR: cannot find 
/home/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/rh/cortex/fwhm36/pos/th40/mc-z.csd


Regards,
Xiaoxu


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Greve, Douglas N.,Ph.D.
Sent: Wednesday, January 13, 2021 9:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_glmfit-sim error with no csd files generated

When you use --cache, mri_glmfit-sim will use precomputed (ie, "cached") CSD 
files as found in  $FREESURFER_HOME/average/mult-comp-cor
On 1/5/2021 4:55 PM, Na, Xiaoxu wrote:

External Email - Use Caution
Dear Freesurfer Experts,

I've all the subjects successfully done recon-all, lgi before coming to the 
group analysis. The following group analysis will use the 10mm smoothing as 
generated in previous recon-all.  Mris_preproc were implemented successfully 
and mri_glmfit as well. However, while coming to the mri_glmfit-sim, it showed 
done finally, but when going back to the directory, I found out no csd files 
have ever been generated, and this was reported as well during the 
mri_glmfit-sim run. Please kindly see the log as below for details. The error 
was reported in the middle, so I changed it into red. It's quite appreciated it 
you may help on this. Thanks a lot!


$ mri_glmfit-sim \
>  --glmdir s/lh.area.g2v3gaCSHQ.10.glmdir \
>  --cache 4 neg \
>  --cwp 0.05  \
>  --2spaces
cmdline mri_glmfit --y sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --fsgd 
sAnalysis/g2v3gaCSHQ.fsgd --C sAnalysis/g1g2.sscorewithBMI.mtx --surf fsaverage 
lh --cortex --glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir
SURFACE: fsaverage lh
log file is sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/cache.mri_glmfit-sim.log

cd /home/xiaoxu/8YearOldNiiB1
/home/xiaoxu/freesurfer/bin/mri_glmfit-sim
--glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir --cache 4 neg --cwp 0.05 
--2spaces

mri_glmfit-sim 7.1.0
Tue Jan  5 15:11:00 CST 2021
Linux xnVMUbuntu18 5.4.0-58-generic #64~18.04.1-Ubuntu SMP Wed Dec 9 17:11:11 
UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
xiaoxu
setenv SUBJECTS_DIR /home/xiaoxu/8YearOldNiiB1
FREESURFER_HOME /home/xiaoxu/freesurfer

Original mri_glmfit command line:
cmdline mri_glmfit --y sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --fsgd 
sAnalysis/g2v3gaCSHQ.fsgd --C sAnalysis/g1g2.sscorewithBMI.mtx --surf fsaverage 
lh --cortex --glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 20.731766
CSD 
/home/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/neg/th40/mc-z.csd
mri_surfcluster --in 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/sig.mgh --mask 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/mask.mgh --cwsig 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.mgh
 --sum 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.summary
 --ocn 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.mgh
 --annot aparc --cwpvalthresh 0.05 --o 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.masked.mgh
 --no-fixmni --csd-out 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/csd

Re: [Freesurfer] mri_glmfit-sim error with no csd files generated

[Greve, Douglas N.,Ph.D.]

When you use --cache, mri_glmfit-sim will use precomputed (ie, "cached") CSD 
files as found in  $FREESURFER_HOME/average/mult-comp-cor

On 1/5/2021 4:55 PM, Na, Xiaoxu wrote:

External Email - Use Caution
Dear Freesurfer Experts,

I’ve all the subjects successfully done recon-all, lgi before coming to the 
group analysis. The following group analysis will use the 10mm smoothing as 
generated in previous recon-all.  Mris_preproc were implemented successfully 
and mri_glmfit as well. However, while coming to the mri_glmfit-sim, it showed 
done finally, but when going back to the directory, I found out no csd files 
have ever been generated, and this was reported as well during the 
mri_glmfit-sim run. Please kindly see the log as below for details. The error 
was reported in the middle, so I changed it into red. It’s quite appreciated it 
you may help on this. Thanks a lot!


$ mri_glmfit-sim \
>  --glmdir s/lh.area.g2v3gaCSHQ.10.glmdir \
>  --cache 4 neg \
>  --cwp 0.05  \
>  --2spaces
cmdline mri_glmfit --y sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --fsgd 
sAnalysis/g2v3gaCSHQ.fsgd --C sAnalysis/g1g2.sscorewithBMI.mtx --surf fsaverage 
lh --cortex --glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir
SURFACE: fsaverage lh
log file is sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/cache.mri_glmfit-sim.log

cd /home/xiaoxu/8YearOldNiiB1
/home/xiaoxu/freesurfer/bin/mri_glmfit-sim
--glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir --cache 4 neg --cwp 0.05 
--2spaces

mri_glmfit-sim 7.1.0
Tue Jan  5 15:11:00 CST 2021
Linux xnVMUbuntu18 5.4.0-58-generic #64~18.04.1-Ubuntu SMP Wed Dec 9 17:11:11 
UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
xiaoxu
setenv SUBJECTS_DIR /home/xiaoxu/8YearOldNiiB1
FREESURFER_HOME /home/xiaoxu/freesurfer

Original mri_glmfit command line:
cmdline mri_glmfit --y sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --fsgd 
sAnalysis/g2v3gaCSHQ.fsgd --C sAnalysis/g1g2.sscorewithBMI.mtx --surf fsaverage 
lh --cortex --glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 20.731766
CSD 
/home/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/neg/th40/mc-z.csd
mri_surfcluster --in 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/sig.mgh --mask 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/mask.mgh --cwsig 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.mgh
 --sum 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.summary
 --ocn 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.mgh
 --annot aparc --cwpvalthresh 0.05 --o 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.masked.mgh
 --no-fixmni --csd-out 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/csd/all.cache.th40.neg-g1g2.sscorewithBMI.csd
 --csd 
/home/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/neg/th40/mc-z.csd
 --csdpdf 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.pdf.dat
 --vwsig 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.voxel.mgh
 --vwsigmax 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.voxel.max.dat
 --oannot 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.annot
 --bonferroni 2 --surf white
Merging CSD files
ERROR: could not open 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/csd/all.cache.th40.neg-g1g2.sscorewithBMI.csd
Creating CDFs from CSD files
csd->threshsign = -1
thsign = neg, id = -1
version 7.1.0
hemi   = lh
srcid  = 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/sig.mgh
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = neg
thmin  = 4
thmax  = -1
fdr= -1
minarea= 0
Bonferroni  = 2
xfmfile= talairach.xfm
nth = -1
outid= 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.masked.mgh
 MGH
ocnid= 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.mgh
 MGH
sumfile  = 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.summary
subjectsdir= /home/xiaoxu/8YearOldNiiB1
FixMNI = 0
Found 148772 vertices in mask
Found 148772 vertices in mask
Found 148772 points in clabel.
- XFM matrix (RAS2RAS) ---
/home/xiaoxu/8YearOldNiiB1/fsaverage/mri/transforms/talairach.xfm
1.0   0.0   0.0   0.0;
0.0   1.0   0.0   0.0;
0.0   0.0   1.0   0.0;
0.0   0.0   0.0   1.0;

Reading source surface /home/xiaoxu/8YearOldNiiB1/fsaverage/surf/lh.white
Done reading source surface
Reading annotation /home/xiaoxu/8YearOldNiiB1/fsaverage/label/lh.aparc.annot
mri_surfcluster supposed to be reproducible but seed not set
reading colortable from annotation file..

[Freesurfer] mri_glmfit-sim error with no csd files generated

[Na, Xiaoxu]

External Email - Use Caution

Dear Freesurfer Experts,

I've all the subjects successfully done recon-all, lgi before coming to the 
group analysis. The following group analysis will use the 10mm smoothing as 
generated in previous recon-all.  Mris_preproc were implemented successfully 
and mri_glmfit as well. However, while coming to the mri_glmfit-sim, it showed 
done finally, but when going back to the directory, I found out no csd files 
have ever been generated, and this was reported as well during the 
mri_glmfit-sim run. Please kindly see the log as below for details. The error 
was reported in the middle, so I changed it into red. It's quite appreciated it 
you may help on this. Thanks a lot!


$ mri_glmfit-sim \
>  --glmdir s/lh.area.g2v3gaCSHQ.10.glmdir \
>  --cache 4 neg \
>  --cwp 0.05  \
>  --2spaces
cmdline mri_glmfit --y sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --fsgd 
sAnalysis/g2v3gaCSHQ.fsgd --C sAnalysis/g1g2.sscorewithBMI.mtx --surf fsaverage 
lh --cortex --glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir
SURFACE: fsaverage lh
log file is sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/cache.mri_glmfit-sim.log

cd /home/xiaoxu/8YearOldNiiB1
/home/xiaoxu/freesurfer/bin/mri_glmfit-sim
--glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir --cache 4 neg --cwp 0.05 
--2spaces

mri_glmfit-sim 7.1.0
Tue Jan  5 15:11:00 CST 2021
Linux xnVMUbuntu18 5.4.0-58-generic #64~18.04.1-Ubuntu SMP Wed Dec 9 17:11:11 
UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
xiaoxu
setenv SUBJECTS_DIR /home/xiaoxu/8YearOldNiiB1
FREESURFER_HOME /home/xiaoxu/freesurfer

Original mri_glmfit command line:
cmdline mri_glmfit --y sAnalysis/lh.area.g2v3gaCSHQ.10.mgh --fsgd 
sAnalysis/g2v3gaCSHQ.fsgd --C sAnalysis/g1g2.sscorewithBMI.mtx --surf fsaverage 
lh --cortex --glmdir sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir

DoSim = 0
UseCache = 1
DoPoll = 0
DoPBSubmit = 0
DoBackground = 0
DiagCluster = 0
gd2mtx = dods
fwhm = 20.731766
CSD 
/home/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/neg/th40/mc-z.csd
mri_surfcluster --in 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/sig.mgh --mask 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/mask.mgh --cwsig 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.mgh
 --sum 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.summary
 --ocn 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.mgh
 --annot aparc --cwpvalthresh 0.05 --o 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.masked.mgh
 --no-fixmni --csd-out 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/csd/all.cache.th40.neg-g1g2.sscorewithBMI.csd
 --csd 
/home/xiaoxu/freesurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm21/neg/th40/mc-z.csd
 --csdpdf 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.pdf.dat
 --vwsig 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.voxel.mgh
 --vwsigmax 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.voxel.max.dat
 --oannot 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.annot
 --bonferroni 2 --surf white
Merging CSD files
ERROR: could not open 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/csd/all.cache.th40.neg-g1g2.sscorewithBMI.csd
Creating CDFs from CSD files
csd->threshsign = -1
thsign = neg, id = -1
version 7.1.0
hemi   = lh
srcid  = 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/sig.mgh
srcsubjid  = fsaverage
srcsurf= white
srcframe   = 0
thsign = neg
thmin  = 4
thmax  = -1
fdr= -1
minarea= 0
Bonferroni  = 2
xfmfile= talairach.xfm
nth = -1
outid= 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.masked.mgh
 MGH
ocnid= 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.ocn.mgh
 MGH
sumfile  = 
sAnalysis/lh.area.g2v3gaCSHQ.10.glmdir/g1g2.sscorewithBMI/cache.th40.neg.sig.cluster.summary
subjectsdir= /home/xiaoxu/8YearOldNiiB1
FixMNI = 0
Found 148772 vertices in mask
Found 148772 vertices in mask
Found 148772 points in clabel.
- XFM matrix (RAS2RAS) ---
/home/xiaoxu/8YearOldNiiB1/fsaverage/mri/transforms/talairach.xfm
1.0   0.0   0.0   0.0;
0.0   1.0   0.0   0.0;
0.0   0.0   1.0   0.0;
0.0   0.0   0.0   1.0;

Reading source surface /home/xiaoxu/8YearOldNiiB1/fsaverage/surf/lh.white
Done reading source surface
Reading annotation /home/xiaoxu/8YearOldNiiB1/fsaverage/label/lh.aparc.annot
mri_surfcluster supposed to be reproducible but seed not set
reading colortable from annotation file...
colortable with 36 entries read (originally 
/autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
Computing metric properties
Loa

Re: [Freesurfer] mri_glmfit-sim error CSDs have the same seed

[Meaghan Perdue]

External Email - Use Caution

Hi Doug,

Deleting the .csd files and re-running worked.
Thank you!
Meaghan

On Tue, Sep 15, 2020 at 11:30 AM Douglas N. Greve 
wrote:

> *Message sent from a system outside of UConn.*
>
> Hmm, there should have been a lot more terminal output than that.
> Try this, delete the CSD files:
> rm lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j*-osgm.csd
> Then re-run. If it fails, then send me the perm.th20.abs.j*-osgm.csd files
>
> On 9/14/2020 2:58 PM, Meaghan Perdue wrote:
>
> External Email - Use Caution
> Hi Doug,
>
> Here is the command:
>
> mri_glmfit-sim --glmdir lh.rs6980093.thickness10.glmdir --perm 1000 2.0
> abs --cwp 0.05 --2spaces --bg 4
>
> And here is the output:
>
> mri_glmfit simulation done 4.78645
>
>
> mri_glmfit simulation done 4.806
>
>
> mri_glmfit simulation done 4.81553
>
>
> mri_glmfit simulation done 4.81997
>
>
> mri_surfcluster --in
> lh.rs6980093.thickness10.glmdir/rs6980093_thickness/sig.mgh --mask
> lh.rs6980093.thickness10.glmdir/mask.mgh --cwsig
> lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.cluster.mgh
> --sum
> lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.cluster.summary
> --ocn
> lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.ocn.mgh
> --annot aparc --cwpvalthresh 0.05 --o
> lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.masked.mgh
> --no-fixmni --csd
> lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j001-rs6980093_thickness.csd
> --csd
> lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j002-rs6980093_thickness.csd
> --csd
> lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j003-rs6980093_thickness.csd
> --csd
> lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j004-rs6980093_thickness.csd
> --csdpdf
> lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.pdf.dat
> --vwsig
> lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.voxel.mgh
> --vwsigmax
> lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.voxel.max.dat
> --oannot
> lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.ocn.annot
> --bonferroni 2 --surf white
> ERROR: CSDmerge: CSDs have same seed
>
>
> Thank you!
> Meaghan
>
> On Wed, Sep 9, 2020 at 4:28 PM Douglas N. Greve 
> wrote:
>
>> *Message sent from a system outside of UConn.*
>>
>> please send the full command line and terminal output
>>
>> On 9/9/2020 3:19 PM, Meaghan Perdue wrote:
>>
>> External Email - Use Caution
>> Hello Freesurfer experts,
>>
>> We're receiving the following error message when trying to run
>> mri_glmfit-sim:
>> ERROR: CSDmerge: CSDs have same seed
>>
>> This only occurs when we try to run the permutation on the LH for
>> thickness. We've been able to run the simulation successfully on LH surface
>> area and RH thickness and area.
>>
>> How can we troubleshoot this problem?
>>
>> Thank you,
>> Meaghan Perdue
>>
>> --
>> Meaghan Perdue
>> she | her | hers
>>
>> PhD Student
>> Developmental Psychology
>> Neurobiology of Language
>> University of Connecticut
>> Bousfield A302
>> Visit my website 
>>
>> ___
>> Freesurfer mailing 
>> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> --
> Meaghan Perdue
> she | her | hers
>
> PhD Student
> Developmental Psychology
> Neurobiology of Language
> University of Connecticut
> Bousfield A302
> Visit my website 
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 
Meaghan Perdue
she | her | hers

PhD Student
Developmental Psychology
Neurobiology of Language
University of Connecticut
Bousfield A302
Visit my website 
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] mri_glmfit-sim error CSDs have the same seed

[Douglas N. Greve]

Hmm, there should have been a lot more terminal output than that.
Try this, delete the CSD files:
rm lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j*-osgm.csd
Then re-run. If it fails, then send me the perm.th20.abs.j*-osgm.csd files

On 9/14/2020 2:58 PM, Meaghan Perdue wrote:


External Email - Use Caution

Hi Doug,

Here is the command:

mri_glmfit-sim --glmdir lh.rs6980093.thickness10.glmdir --perm 1000 
2.0 abs --cwp 0.05 --2spaces --bg 4


And here is the output:

mri_glmfit simulation done 4.78645


mri_glmfit simulation done 4.806


mri_glmfit simulation done 4.81553


mri_glmfit simulation done 4.81997


mri_surfcluster --in 
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/sig.mgh --mask 
lh.rs6980093.thickness10.glmdir/mask.mgh --cwsig 
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.cluster.mgh 
--sum 
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.cluster.summary 
--ocn 
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.ocn.mgh 
--annot aparc --cwpvalthresh 0.05 --o 
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.masked.mgh 
--no-fixmni --csd 
lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j001-rs6980093_thickness.csd 
--csd 
lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j002-rs6980093_thickness.csd 
--csd 
lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j003-rs6980093_thickness.csd 
--csd 
lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j004-rs6980093_thickness.csd 
--csdpdf 
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.pdf.dat 
--vwsig 
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.voxel.mgh 
--vwsigmax 
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.voxel.max.dat 
--oannot 
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.ocn.annot 
--bonferroni 2 --surf white

ERROR: CSDmerge: CSDs have same seed


Thank you!
Meaghan

On Wed, Sep 9, 2020 at 4:28 PM Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu>> wrote:


*Message sent from a system outside of UConn.*

please send the full command line and terminal output

On 9/9/2020 3:19 PM, Meaghan Perdue wrote:


External Email - Use Caution

Hello Freesurfer experts,

We're receiving the following error message when trying to run
mri_glmfit-sim:
ERROR: CSDmerge: CSDs have same seed

This only occurs when we try to run the permutation on the LH for
thickness. We've been able to run the simulation successfully on
LH surface area and RH thickness and area.

How can we troubleshoot this problem?

Thank you,
Meaghan Perdue

-- 
Meaghan Perdue

she | her | hers

PhD Student
Developmental Psychology
Neurobiology of Language
University of Connecticut
Bousfield A302
Visit my website 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu  
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
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Freesurfer@nmr.mgh.harvard.edu 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



--
Meaghan Perdue
she | her | hers

PhD Student
Developmental Psychology
Neurobiology of Language
University of Connecticut
Bousfield A302
Visit my website 

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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Re: [Freesurfer] mri_glmfit-sim error CSDs have the same seed

[Meaghan Perdue]

External Email - Use Caution

Hi Doug,

Here is the command:

mri_glmfit-sim --glmdir lh.rs6980093.thickness10.glmdir --perm 1000 2.0 abs
--cwp 0.05 --2spaces --bg 4

And here is the output:

mri_glmfit simulation done 4.78645


mri_glmfit simulation done 4.806


mri_glmfit simulation done 4.81553


mri_glmfit simulation done 4.81997


mri_surfcluster --in
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/sig.mgh --mask
lh.rs6980093.thickness10.glmdir/mask.mgh --cwsig
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.cluster.mgh
--sum
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.cluster.summary
--ocn
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.ocn.mgh
--annot aparc --cwpvalthresh 0.05 --o
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.masked.mgh
--no-fixmni --csd
lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j001-rs6980093_thickness.csd
--csd
lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j002-rs6980093_thickness.csd
--csd
lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j003-rs6980093_thickness.csd
--csd
lh.rs6980093.thickness10.glmdir/csd/perm.th20.abs.j004-rs6980093_thickness.csd
--csdpdf
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.pdf.dat
--vwsig
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.voxel.mgh
--vwsigmax
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.voxel.max.dat
--oannot
lh.rs6980093.thickness10.glmdir/rs6980093_thickness/perm.th20.abs.sig.ocn.annot
--bonferroni 2 --surf white
ERROR: CSDmerge: CSDs have same seed


Thank you!
Meaghan

On Wed, Sep 9, 2020 at 4:28 PM Douglas N. Greve 
wrote:

> *Message sent from a system outside of UConn.*
>
> please send the full command line and terminal output
>
> On 9/9/2020 3:19 PM, Meaghan Perdue wrote:
>
> External Email - Use Caution
> Hello Freesurfer experts,
>
> We're receiving the following error message when trying to run
> mri_glmfit-sim:
> ERROR: CSDmerge: CSDs have same seed
>
> This only occurs when we try to run the permutation on the LH for
> thickness. We've been able to run the simulation successfully on LH surface
> area and RH thickness and area.
>
> How can we troubleshoot this problem?
>
> Thank you,
> Meaghan Perdue
>
> --
> Meaghan Perdue
> she | her | hers
>
> PhD Student
> Developmental Psychology
> Neurobiology of Language
> University of Connecticut
> Bousfield A302
> Visit my website 
>
> ___
> Freesurfer mailing 
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>
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-- 
Meaghan Perdue
she | her | hers

PhD Student
Developmental Psychology
Neurobiology of Language
University of Connecticut
Bousfield A302
Visit my website 
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Re: [Freesurfer] mri_glmfit-sim error CSDs have the same seed

[Douglas N. Greve]

please send the full command line and terminal output

On 9/9/2020 3:19 PM, Meaghan Perdue wrote:


External Email - Use Caution

Hello Freesurfer experts,

We're receiving the following error message when trying to run 
mri_glmfit-sim:

ERROR: CSDmerge: CSDs have same seed

This only occurs when we try to run the permutation on the LH for 
thickness. We've been able to run the simulation successfully on LH 
surface area and RH thickness and area.


How can we troubleshoot this problem?

Thank you,
Meaghan Perdue

--
Meaghan Perdue
she | her | hers

PhD Student
Developmental Psychology
Neurobiology of Language
University of Connecticut
Bousfield A302
Visit my website 

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Re: [Freesurfer] mri_glmfit-sim using --cwp 0.05, --cwp 0.1, --cwp 0.999

[Douglas N. Greve]

  0.09940 and 0.10338 seem pretty close to me:). The summary file has Hi and 
Low which is the 95% confidence interval assuming a binomial model at the mean 
prob



On 9/9/2020 3:24 PM, freesurferl...@gmx.com wrote:
>  External Email - Use Caution
>
> Thanks, I was looking for the higher resolution as, from my understanding, 
> the p-value of a cluster is usually reported as “p =“ rather than “p <“ (but 
> this may be not worth the extra computational time for cluster 1).
>
> Just as a follow up question, what about cluster 2 for cwp0.1 and cwp0.999. 
> This has a CWP of 0.09940 and 0.10338 respectively. Should we be expecting 
> convergence by 10,000 iterations for this cluster?
>
>
>
> On 10/9/20 at 12:18 am, Douglas N. Greve wrote:
>
> The issue is that the chance of this event happening by chance is very
> low, around 2-14 times out of 10,000. You are getting this variation
> because you are only using 1 iterations. But why would you need
> higher resolution to your p-value? It will definitely be below 0.05
> needed for publication.
>
> On 9/8/2020 8:45 PM, Paul wrote:
>>  External Email - Use Caution
>>
>> Dear Douglas,
>> Thanks for looking in this. Please see files attached.
>> Also, I have used Freesurfer 5.1 for all the processing (i.e recon-all
>> and editing etc) and have used Freesurfer 6.0 for the statistical
>> analysis (i.e. mris_preproc, mri_surf2surf, mri_glmfit) and the patch
>> version of mri_glmfit-sim (i.e
>> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/mri_glmfit-sim).
>> <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/mri_glmfit-sim>
>> Kind regards,
>> Paul
>> *Sent:* Wednesday, September 09, 2020 at 1:01 AM
>> *From:* "Douglas N. Greve" 
>> *To:* freesurfer@nmr.mgh.harvard.edu
>> *Subject:* Re: [Freesurfer] mri_glmfit-sim using --cwp 0.05, --cwp
>> 0.1, --cwp 0.999
>> On 9/7/2020 10:52 PM, Paul wrote:
>>
>>  External Email - Use Caution
>>
>>  Dear Freesurfer Experts,
>>  I have few questions regarding CWP values from mri_glmfit-sim
>>  using --cwp 0.05, --cwp 0.1, --cwp 0.999.
>>  Using the 3 three commands below (A, B and C):
>>  A. mri_glmfit-sim  --glmdir lh_status.glmdir --perm 1 1.3 abs
>>  --cwp 0.05 --2spaces --bg 1
>>  B. mri_glmfit-sim  --glmdir lh_status.glmdir --perm 1 1.3 abs
>>  --cwp 0.1 --2spaces --bg 1
>>  C. mri_glmfit-sim  --glmdir lh_status.glmdir --perm 1 1.3 abs
>>  --cwp 0.999 --2spaces --bg 1
>>  I end up with the same significant ClusterNo 1.  (in terms of Max,
>>  VtxMax, Size(mm^2), MNIX, MNIY, MNIZ, NVtxs, WghtVtx, Annot)
>>  However, the CWP is 0.00040, 0.00140, and 0.00020 for A, B and C
>>  respetively.
>>  I was expected after 10,000 iterations, the CWP would be more
>>  closely matched or even convergent.
>>  Could you please let me know if this result is typical after
>>  10,000 iterations?
>>  Also, should I be using more iterations (say 20k or more 100k?) to
>>  reach convergence across A, B, and C or is it usual to just report
>>  A, B or C?
>>
>> I don't understand. All you are changing is the CWP threshold? The
>> final CWP value for a cluster should not be changing at all. If this
>> is the case, can you send me the summary file for each?
>>
>>  Kind regards,
>>  Paul
>>
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[Freesurfer] mri_glmfit-sim error CSDs have the same seed

[Meaghan Perdue]

External Email - Use Caution

Hello Freesurfer experts,

We're receiving the following error message when trying to run
mri_glmfit-sim:
ERROR: CSDmerge: CSDs have same seed

This only occurs when we try to run the permutation on the LH for
thickness. We've been able to run the simulation successfully on LH surface
area and RH thickness and area.

How can we troubleshoot this problem?

Thank you,
Meaghan Perdue

-- 
Meaghan Perdue
she | her | hers

PhD Student
Developmental Psychology
Neurobiology of Language
University of Connecticut
Bousfield A302
Visit my website 
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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