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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 dgreve@mgh.harvard.edu님이 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/1czZRw3EoQx6OvftUtPfBxAe8r0M8EZljAEkQmJk1CUdUwV... 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 faces 327680 Total area 65417.000000 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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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 dgreve@mgh.harvard.edu님이 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 dgreve@mgh.harvard.edu님이 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_... 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 faces 327680 Total area 65417.000000 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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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 dgreve@mgh.harvard.edu님이 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 dgreve@mgh.harvard.edu님이 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 dgreve@mgh.harvard.edu님이 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-zahadD2Ew... 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 faces 327680 Total area 65417.000000 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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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 hwj418418@gmail.com님이 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
<dgreve@mgh.harvard.edu>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
    <dgreve@mgh.harvard.edu>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
        <dgreve@mgh.harvard.edu>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*
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            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         65417.000000
            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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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... 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 dgreve@mgh.harvard.edu님이 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 <hwj418418@gmail.com>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
    <dgreve@mgh.harvard.edu>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
        <dgreve@mgh.harvard.edu>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
            <dgreve@mgh.harvard.edu>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
                <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 faces    327680
                Total area 65417.000000
                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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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 hwj418418@gmail.com님이 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 dgreve@mgh.harvard.edu님이 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 dgreve@mgh.harvard.edu님이 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 dgreve@mgh.harvard.edu님이 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_bSOoLiPouSFm... 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 faces 327680 Total area 65417.000000 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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Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1z3EH_59ofNcQNR1_Aw_q8DsKQj2gwuN6MAIrf7Q3Fc8gxn... https://secure-web.cisco.com/1ulpvinyitIUSvjVtOCospKw5F9QAk0aSUu1I9W0LT9zZqmeQh0j3i1_P6BDSKt9FQjGQKm1GLvIR1BUwY6m2WYtmeOqyzUnOC-YSYOCYL_9mXf_yQRucxrykULk2wcgH_NoLncDJEd0o6cqq11JbusP1mncbZfaoT_j0orTXHlQj-NwJdkLeOzR75SznpiPkXIgl4IgTNjMSlgrIhmUwRmWkzOibNYL9WO5NQF5lgYoS0cSkAWhsMhRgVbfVR4DvDBbafLXgiMd1G3rfg15yqTGSAkljmzU9rAyrGCl-0VI0yv8pFnaGMWTRmTVqzA8IRseXLucArSyF4C_qGbp7IA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1z3EH_59ofNcQNR1_Aw_q8DsKQj2gwuN6MAIrf7Q3Fc8gxn... https://secure-web.cisco.com/1ulpvinyitIUSvjVtOCospKw5F9QAk0aSUu1I9W0LT9zZqmeQh0j3i1_P6BDSKt9FQjGQKm1GLvIR1BUwY6m2WYtmeOqyzUnOC-YSYOCYL_9mXf_yQRucxrykULk2wcgH_NoLncDJEd0o6cqq11JbusP1mncbZfaoT_j0orTXHlQj-NwJdkLeOzR75SznpiPkXIgl4IgTNjMSlgrIhmUwRmWkzOibNYL9WO5NQF5lgYoS0cSkAWhsMhRgVbfVR4DvDBbafLXgiMd1G3rfg15yqTGSAkljmzU9rAyrGCl-0VI0yv8pFnaGMWTRmTVqzA8IRseXLucArSyF4C_qGbp7IA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1z3EH_59ofNcQNR1_Aw_q8DsKQj2gwuN6MAIrf7Q3Fc8gxn...