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

2022-02-13 Thread 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
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Re: [Freesurfer] mri_glmfit error: MatrixMultiplyD(): m2 is null

2022-02-14 Thread 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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

2022-02-14 Thread 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 error: MatrixMultiplyD(): m2 is null

2022-02-16 Thread 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

___
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

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

2022-02-16 Thread 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

2022-02-16 Thread 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

2022-02-16 Thread 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

2022-02-21 Thread 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 error: MatrixMultiplyD(): m2 is null

2022-02-24 Thread 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 error: MatrixMultiplyD(): m2 is null

2022-02-25 Thread 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

2022-02-25 Thread 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

2022-03-09 Thread 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

2022-03-09 Thread 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