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

[Douglas N. Greve]

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

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


External Email - Use Caution

Hello,

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


I have attached the necessary files in the email below.

Many thanks,
Miracle

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


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

[miracle ozzoude]

External Email - Use Caution

Hello,

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

I have attached the necessary files in the email below.

Many thanks,
Miracle

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

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

Re: [Freesurfer] mri_glmfit error

[Douglas N. Greve]

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


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


External Email - Use Caution

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

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


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

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

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



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

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Re: [Freesurfer] mri_glmfit error

[fernanda rohrsetzer]

External Email - Use Caution

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



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

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

Re: [Freesurfer] mri_glmfit error

[Douglas N. Greve]

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


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


External Email - Use Caution

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



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


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


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



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


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

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


External Email - Use Caution

I'm so sorry...

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

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


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


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


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


glmfit:


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


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


Thank you so much!!!
Fernanda

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

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

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


External Email - Use Caution

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

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

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

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

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Re: [Freesurfer] mri_glmfit error

[fernanda rohrsetzer]

External Email - Use Caution

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


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


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


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



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

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

[Douglas N. Greve]

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

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


External Email - Use Caution

I'm so sorry...

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

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



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


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


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


glmfit:


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



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


Thank you so much!!!
Fernanda

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


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

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


External Email - Use Caution

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

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

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

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

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The information in this e-mail is 

Re: [Freesurfer] mri_glmfit error

[Douglas N. Greve]

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

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


External Email - Use Caution

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

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

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

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

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

[Freesurfer] mri_glmfit error

[fernanda rohrsetzer]

External Email - Use Caution

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

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

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

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

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

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

[Piot, Alex]

External Email - Use Caution

Thanks so much, Doug that worked!


--

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



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

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


⚠ Caution: External sender

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

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

External Email - Use Caution

Hello Freesurfer experts,

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

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

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

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

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

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

Freesurfer version: 7.2.0, Ubuntu 20.04, Windows WSL

Best wishes,
Alex

--

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

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

[Douglas N. Greve]

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


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


External Email - Use Caution

Hello Freesurfer experts,

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



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

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

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


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


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

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

Freesurfer version: 7.2.0, Ubuntu 20.04, Windows WSL

Best wishes,
Alex

--

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





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

[Piot, Alex]

External Email - Use Caution

Hello Freesurfer experts,

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

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

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

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

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

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

Freesurfer version: 7.2.0, Ubuntu 20.04, Windows WSL

Best wishes,
Alex

--

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

 -- UCL
UNITy 
Project




mri_glmfit.log
Description: mri_glmfit.log


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

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

Re: [Freesurfer] mri_glmfit error

[Douglas N. Greve]

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


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


External Email - Use Caution

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

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

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


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

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



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

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

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


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

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

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





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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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 .
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continue to communicate over unencrypted e-mail. 

[Freesurfer] mri_glmfit error

[David]

External Email - Use Caution

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

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


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

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

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



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


ERROR: cannot find residual group66.area_66sm.lh/eres needed with --perm-resid
  when running mri_glmfit, make sure to include --eres-save
ERROR: cannot find residual group66.area_66sm.rh/eres needed with --perm-resid
  when running mri_glmfit, make sure to include --eres-save
glm66.sh: line 14: --perm-resid: command not found
---
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

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

[정현우]

External Email - Use Caution

Hi Dr. Greve,

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

I genuinely appreciate your support!

Best,
Hyunwoo Jeong

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

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

 On 2/16/2022 10:53 AM, 정현우 wrote:

 External Email - Use Caution
 Hi Dr. Greve,

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

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

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

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

 Thanks,
 Hyunwoo Jeong

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

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

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

[Douglas N. Greve]

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



On 2/25/2022 8:07 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

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


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



Thank you in advance,
Hyunwoo Jeong.



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


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

On 2/21/2022 10:24 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

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

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

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

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

Best,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 10:18, 정현우 님이
작성:

Hi Dr. Greve,

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

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

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

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

Best,
Hyunwoo Jeong

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

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

On 2/16/2022 10:53 AM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

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

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

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

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

Thanks,
Hyunwoo Jeong

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

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

On 2/14/2022 8:46 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

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

Hyunwoo Jeong

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

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

On 2/14/2022 1:21 AM, 정현우 wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

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

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

[정현우]

External Email - Use Caution

Hi Dr. Greve,

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

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

Thank you in advance,
Hyunwoo Jeong.



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

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

 On 2/14/2022 8:46 PM, 정현우 wrote:

 External Email - Use Caution
 Hi Dr. Greve,

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

 Hyunwoo Jeong

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

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

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

[Douglas N. Greve]

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


On 2/21/2022 10:24 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

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


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


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

Best,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 10:18, 정현우 님이 작성:

Hi Dr. Greve,

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

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

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

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

Best,
Hyunwoo Jeong

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

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

On 2/16/2022 10:53 AM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

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

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

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

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

Thanks,
Hyunwoo Jeong

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

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

On 2/14/2022 8:46 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

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

Hyunwoo Jeong

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

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

On 2/14/2022 1:21 AM, 정현우 wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

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

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

).


I ran the following command:

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

Then I got the following error:

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

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

[정현우]

External Email - Use Caution

Hi Dr. Greve,

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

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

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

Best,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 10:18, 정현우 님이 작성:

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

 On 2/14/2022 1:21 AM, 정현우 wrote:

 External Email - Use Caution
 Hello FreeSurfer Developers,

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

 I ran the following command:

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

 Then I got the following error:

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

 7.2.0
 cwd 

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

[정현우]

External Email - Use Caution

Hi Dr. Greve,

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

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

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

Best,
Hyunwoo Jeong

2022년 2월 17일 (목) 오전 10:18, 정현우 님이 작성:

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

 On 2/14/2022 1:21 AM, 정현우 wrote:

 External Email - Use Caution
 Hello FreeSurfer Developers,

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

 I ran the following command:

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

 Then I got the following error:

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

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

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

[정현우]

External Email - Use Caution

Hi Dr. Greve,

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

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

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

Best,
Hyunwoo Jeong

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

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

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

[Douglas N. Greve]

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


On 2/16/2022 10:53 AM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

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

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


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


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

Thanks,
Hyunwoo Jeong

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


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

On 2/14/2022 8:46 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

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

Hyunwoo Jeong

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

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

On 2/14/2022 1:21 AM, 정현우 wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

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

).


I ran the following command:

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

Then I got the following error:

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

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

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

[정현우]

External Email - Use Caution

Hi Dr. Greve,

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

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

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

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

Thanks,
Hyunwoo Jeong

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

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

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

[Douglas N. Greve]

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


On 2/14/2022 8:46 PM, 정현우 wrote:


External Email - Use Caution

Hi Dr. Greve,

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


Hyunwoo Jeong

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


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

On 2/14/2022 1:21 AM, 정현우 wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

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

).


I ran the following command:

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

Then I got the following error:

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

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

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

I used FreeSurfer version 7.2.0 and Ubuntu 20.04.

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

Thank you in advance,

Hyunwoo Jeong

___
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

[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
> 

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

[Douglas N. Greve]

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

On 2/14/2022 1:21 AM, 정현우 wrote:


External Email - Use Caution

Hello FreeSurfer Developers,

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



I ran the following command:

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


Then I got the following error:

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

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

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

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

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


I used FreeSurfer version 7.2.0 and Ubuntu 20.04.

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


Thank you in advance,

Hyunwoo Jeong

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

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

[정현우]

External Email - Use Caution

Hello FreeSurfer Developers,

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

I ran the following command:

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

Then I got the following error:

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

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

I used FreeSurfer version 7.2.0 and Ubuntu 20.04.

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

Thank you in advance,

Hyunwoo Jeong
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Re: [Freesurfer] mri_glmfit error

[Douglas N. Greve]

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

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


External Email - Use Caution

Hello FS experts,

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


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


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


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

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



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[Freesurfer] mri_glmfit error

[Ishi Tandon AIB, Jaipur]

External Email - Use Caution

Hello FS experts,

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

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

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

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

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


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

[Douglas N. Greve]

Can you send the full terminal output?

On 6/15/2020 10:41 PM, 邓刊 wrote:


External Email - Use Caution

Hello Freesurfer Experts!

I met the  mri_glmfit error:  matrix is ill-conditioned or badly scaled, condno 
= 1e+08.I am trying to run a 8 group 3 variables analysis: with diagnosis being 
my
variable of interest and trying to regress out the effects of 
gender,background,age,education and seizure.
   1. Command line:
   mris_preproc --fsgd qdec/group.fsgd --cache-in 
thickness.fwhm10.fsaverage --target fsaverage --hemi lh --out 
lh.thickness.fwhm10.groups.mgh

mri_glmfit --y lh.thickness.fwhm10.groups.mgh --fsgd group.fsgd dods 
--C Difference.group.mtx --surf fsaverage lh --cortex --glmdir 
fwhm10.thickness.glmdir

   2. The FSGD file (see attached)
   3. And the design matrix:
  1 1 1 1 -1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
(or see attached)

I encounter this error. I have no idea how to proceed.Is all this because I 
have too many covariates?
I am looking forward to your response!
Thanks,


Kan







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[Freesurfer] mri_glmfit error

[邓刊]

External Email - Use Caution

Hello Freesurfer Experts!

I met the  mri_glmfit error:  matrix is ill-conditioned or badly scaled, condno 
= 1e+08.I am trying to run a 8 group 3 variables analysis: with diagnosis being 
my
variable of interest and trying to regress out the effects of 
gender,background,age,education and seizure.  1. Command line:
  mris_preproc --fsgd qdec/group.fsgd --cache-in thickness.fwhm10.fsaverage 
--target fsaverage --hemi lh --out lh.thickness.fwhm10.groups.mgh

   mri_glmfit --y lh.thickness.fwhm10.groups.mgh --fsgd group.fsgd dods --C 
Difference.group.mtx --surf fsaverage lh --cortex --glmdir 
fwhm10.thickness.glmdir 

  2. The FSGD file (see attached)
  3. And the design matrix:
 1 1 1 1 -1 -1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0(or 
see attached)

I encounter this error. I have no idea how to proceed.Is all this because I 
have too many covariates?
I am looking forward to your response!
Thanks,


Kan






 

Difference.group.mtx
Description: Binary data


group.fsgd
Description: Binary data
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Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

[Douglas N. Greve]

This is a design problem that will not be solved by simply forcing 
glmfit to run. I would remove that class and those subjectgs


On 5/13/2020 2:33 PM, Marina Fernández wrote:


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Thank you, Doug.

That makes sense.
Do you think in this case it is a good option to add the flag 
--illcond to run this analysis without getting an error? or is it 
better not to use the variable apoe in these statistical analyzes?

What do you recommend us?

Best wishes,
Marina.

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Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

[Marina Fernández]

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 Thank you, Doug.

That makes sense.
Do you think in this case it is a good option to add the flag --illcond to
run this analysis without getting an error? or is it better not to use the
variable apoe in these statistical analyzes?
What do you recommend us?

Best wishes,
Marina.
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Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

[Douglas N. Greve]

The problem is that class 3 (smaleapoe) only has two members but you 
have four covariates. When you use DODS, each class gets its own fit to 
the data. In this case, class 3 is trying to solve for 5 unkowns (offset 
+ 4 slopes) with only two data points.


On 5/13/2020 10:18 AM, Marina Fernández wrote:


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Hi Douglas,

I email you the fsgd file and I have also sent it through FTP.

Thank you for your attention.

Best regards,
Marina.

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Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

[Marina Fernández]

External Email - Use Caution

Hi Douglas,

I email you the fsgd file and I have also sent it through FTP.

Thank you for your attention.

Best regards,
Marina.
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Re: [Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

[Douglas N. Greve]

Can you email the fsgd file?

On 5/12/2020 1:35 PM, Marina Fernández wrote:


External Email - Use Caution

Dear Freesurfer experts,

I get the error that you can find at the end of this message when I am 
running mri_glmfit.


Whenever I run an analysis in which the experimental design has more 
than 12 columns, I get the same error, whereas if the experimental 
design has less than 12 columns, the analysis is successful.


I also send you the fsgd.txt file (through FTP File Exchange). In this 
file you can see that there are four groups that have been created by 
the combination of two discrete variables (sex and apoe-type).


How can I solve this problem?

Thank you in advance.



ERROR MESSAGE:
(...)

Saving design matrix to 
/usr/local/freesurfer/subjects/amy_frapsaliva_stats/stats/cortex/cortex_caseageeducfrap/pruebax_frapsalgroup_NEG/lh.fsgd_subj_gauss001/Xg.dat

Computing normalized matrix
Normalized matrix condition is 1e+08
Design matrix --
 0.0   1.0   0.0   0.0   0.0   0.83619 0.0   
0.0   0.0   0.91963   0.0   0.0 0.0   0.79984   
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.39700 0.0   
0.0   0.0  -0.73337   0.0   0.0 0.0  -0.84287   
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.74935 0.0   
0.0   0.0   0.91963   0.0   0.0 0.0  -0.82284   
0.0   0.0;
 1.0   0.0   0.0   0.0  -1.45403   0.0 0.0   
0.0  -0.32012   0.0   0.0   0.0 0.17882   0.0   
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.57318 0.0   
0.0   0.0   0.91963   0.0   0.0 0.0   0.33908   
0.0   0.0;
 0.0   0.0   1.0   0.0   0.0   0.0 1.71704   
0.0   0.0   0.0   0.09313   0.0 0.0   0.0 
 -0.02652   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0 0.0   
0.66002   0.0   0.0   0.0  -0.11350 0.0   0.0   
0.0   0.46929;
 0.0   0.0   0.0   1.0   0.0   0.0 0.0   
0.48385   0.0   0.0   0.0  -0.94000 0.0   0.0   
0.0   1.23055;
 0.0   0.0   0.0   1.0   0.0   0.0 0.0   
0.83619   0.0   0.0   0.0  -2.38637 0.0   0.0   
0.0  -0.90297;
 0.0   1.0   0.0   0.0   0.0  -0.04466 0.0   
0.0   0.0   0.91963   0.0   0.0 0.0   0.28399   
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0   0.48385 0.0   
0.0   0.0   0.91963   0.0   0.0 0.0   0.86996   
0.0   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0 0.0   
1.18853   0.0   0.0   0.0   0.91963 0.0   0.0   
0.0   0.18883;
 0.0   1.0   0.0   0.0   0.0  -2.15871 0.0   
0.0   0.0  -0.94000   0.0   0.0 0.0   1.53105   
0.0   0.0;
 1.0   0.0   0.0   0.0  -1.98254   0.0 0.0   
0.0   0.50638   0.0   0.0   0.0 0.73974   0.0   
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -1.45403 0.0   
0.0   0.0   0.50638   0.0   0.0 0.0   0.23391   
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0   0.13151 0.0   
0.0   0.0   0.91963   0.0   0.0 0.0  -0.91298   
0.0   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0 0.0 
 -1.63020   0.0   0.0   0.0   0.09313 0.0   0.0   
0.0   0.78982;
 0.0   1.0   0.0   0.0   0.0   0.66002 0.0   
0.0   0.0  -1.55987   0.0   0.0 0.0  -0.15173   
0.0   0.0;
 1.0   0.0   0.0   0.0   1.54087   0.0 0.0   
0.0  -0.32012   0.0   0.0   0.0 1.28564   0.0   
0.0   0.0;
 0.0   0.0   1.0   0.0   0.0   0.0 0.30768   
0.0   0.0   0.0  -0.94000   0.0 0.0   0.0 
 -0.76775   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0 0.0   
1.71704   0.0   0.0   0.0   0.50638 0.0   0.0   
0.0   1.41085;
 0.0   0.0   0.0   1.0   0.0   0.0 0.0   
0.48385   0.0   0.0   0.0  -0.52675 0.0   0.0   
0.0   0.73974;
 1.0   0.0   0.0   0.0  -0.92552   0.0 0.0   
0.0   1.53950   0.0   0.0   0.0  -0.76274   0.0   
0.0   0.0;
 1.0   0.0   0.0   0.0   0.66002   0.0 0.0   
0.0   0.91963   0.0   0.0   0.0  -0.50731   0.0   
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.39700 0.0   
0.0   0.0  -0.94000   0.0   0.0 0.0  -0.93803   
0.0   0.0;
 1.0   0.0   0.0   0.0  -0.04466   

[Freesurfer] mri_glmfit ERROR: matrix is ill-conditioned or badly scaled -

[Marina Fernández]

External Email - Use Caution

Dear Freesurfer experts,

I get the error that you can find at the end of this message when I am
running mri_glmfit.

Whenever I run an analysis in which the experimental design has more than
12 columns, I get the same error, whereas if the experimental design has
less than 12 columns, the analysis is successful.

I also send you the fsgd.txt file (through FTP File Exchange). In this file
you can see that there are four groups that have been created by the
combination of two discrete variables (sex and apoe-type).

How can I solve this problem?

Thank you in advance.



ERROR MESSAGE:
(...)

Saving design matrix to
/usr/local/freesurfer/subjects/amy_frapsaliva_stats/stats/cortex/cortex_caseageeducfrap/pruebax_frapsalgroup_NEG/lh.fsgd_subj_gauss001/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1e+08
Design matrix --
 0.0   1.0   0.0   0.0   0.0   0.83619   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.79984
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.39700   0.0
0.0   0.0  -0.73337   0.0   0.0   0.0  -0.84287
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.74935   0.0
0.0   0.0   0.91963   0.0   0.0   0.0  -0.82284
0.0   0.0;
 1.0   0.0   0.0   0.0  -1.45403   0.0   0.0
0.0  -0.32012   0.0   0.0   0.0   0.17882   0.0
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.57318   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.33908
0.0   0.0;
 0.0   0.0   1.0   0.0   0.0   0.0   1.71704
0.0   0.0   0.0   0.09313   0.0   0.0   0.0
 -0.02652   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.66002   0.0   0.0   0.0  -0.11350   0.0   0.0
0.0   0.46929;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.48385   0.0   0.0   0.0  -0.94000   0.0   0.0
0.0   1.23055;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.83619   0.0   0.0   0.0  -2.38637   0.0   0.0
0.0  -0.90297;
 0.0   1.0   0.0   0.0   0.0  -0.04466   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.28399
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0   0.48385   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.86996
0.0   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
1.18853   0.0   0.0   0.0   0.91963   0.0   0.0
0.0   0.18883;
 0.0   1.0   0.0   0.0   0.0  -2.15871   0.0
0.0   0.0  -0.94000   0.0   0.0   0.0   1.53105
0.0   0.0;
 1.0   0.0   0.0   0.0  -1.98254   0.0   0.0
0.0   0.50638   0.0   0.0   0.0   0.73974   0.0
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -1.45403   0.0
0.0   0.0   0.50638   0.0   0.0   0.0   0.23391
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0   0.13151   0.0
0.0   0.0   0.91963   0.0   0.0   0.0  -0.91298
0.0   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
 -1.63020   0.0   0.0   0.0   0.09313   0.0   0.0
0.0   0.78982;
 0.0   1.0   0.0   0.0   0.0   0.66002   0.0
0.0   0.0  -1.55987   0.0   0.0   0.0  -0.15173
0.0   0.0;
 1.0   0.0   0.0   0.0   1.54087   0.0   0.0
0.0  -0.32012   0.0   0.0   0.0   1.28564   0.0
0.0   0.0;
 0.0   0.0   1.0   0.0   0.0   0.0   0.30768
0.0   0.0   0.0  -0.94000   0.0   0.0   0.0
 -0.76775   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
1.71704   0.0   0.0   0.0   0.50638   0.0   0.0
0.0   1.41085;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.48385   0.0   0.0   0.0  -0.52675   0.0   0.0
0.0   0.73974;
 1.0   0.0   0.0   0.0  -0.92552   0.0   0.0
0.0   1.53950   0.0   0.0   0.0  -0.76274   0.0
0.0   0.0;
 1.0   0.0   0.0   0.0   0.66002   0.0   0.0
0.0   0.91963   0.0   0.0   0.0  -0.50731   0.0
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.39700   0.0
0.0   0.0  -0.94000   0.0   0.0   0.0  -0.93803
0.0   0.0;
 1.0   0.0   0.0   0.0  -0.04466   0.0   0.0
0.0   0.29975   0.0   0.0   0.0  -1.07325   0.0
0.0   0.0;
 0.0   1.0   

[Freesurfer] mri_glmfit error

[Marina Fernández]

External Email - Use Caution

 Dear Freesurfer experts,

I get the error that you can find at the end of this message when I am
running mri_glmfit.

Whenever I run an analysis in which the experimental design has more than
12 columns, I get the same error, whereas if the experimental design has
less than 12 columns, the analysis is successful.

I also send you the fsgd.txt file (through FTP File Exchange). In this file
you can see that there are four groups that have been created by the
combination of two discrete variables (sex and apoe-type).

How can I solve this problem?

Thank you in advance.



ERROR MESSAGE:
(...)

Saving design matrix to
/usr/local/freesurfer/subjects/amy_frapsaliva_stats/stats/cortex/cortex_caseageeducfrap/pruebax_frapsalgroup_NEG/lh.fsgd_subj_gauss001/Xg.dat
Computing normalized matrix
Normalized matrix condition is 1e+08
Design matrix --
 0.0   1.0   0.0   0.0   0.0   0.83619   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.79984
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.39700   0.0
0.0   0.0  -0.73337   0.0   0.0   0.0  -0.84287
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.74935   0.0
0.0   0.0   0.91963   0.0   0.0   0.0  -0.82284
0.0   0.0;
 1.0   0.0   0.0   0.0  -1.45403   0.0   0.0
0.0  -0.32012   0.0   0.0   0.0   0.17882   0.0
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.57318   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.33908
0.0   0.0;
 0.0   0.0   1.0   0.0   0.0   0.0   1.71704
0.0   0.0   0.0   0.09313   0.0   0.0   0.0
 -0.02652   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.66002   0.0   0.0   0.0  -0.11350   0.0   0.0
0.0   0.46929;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.48385   0.0   0.0   0.0  -0.94000   0.0   0.0
0.0   1.23055;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.83619   0.0   0.0   0.0  -2.38637   0.0   0.0
0.0  -0.90297;
 0.0   1.0   0.0   0.0   0.0  -0.04466   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.28399
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0   0.48385   0.0
0.0   0.0   0.91963   0.0   0.0   0.0   0.86996
0.0   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
1.18853   0.0   0.0   0.0   0.91963   0.0   0.0
0.0   0.18883;
 0.0   1.0   0.0   0.0   0.0  -2.15871   0.0
0.0   0.0  -0.94000   0.0   0.0   0.0   1.53105
0.0   0.0;
 1.0   0.0   0.0   0.0  -1.98254   0.0   0.0
0.0   0.50638   0.0   0.0   0.0   0.73974   0.0
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -1.45403   0.0
0.0   0.0   0.50638   0.0   0.0   0.0   0.23391
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0   0.13151   0.0
0.0   0.0   0.91963   0.0   0.0   0.0  -0.91298
0.0   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
 -1.63020   0.0   0.0   0.0   0.09313   0.0   0.0
0.0   0.78982;
 0.0   1.0   0.0   0.0   0.0   0.66002   0.0
0.0   0.0  -1.55987   0.0   0.0   0.0  -0.15173
0.0   0.0;
 1.0   0.0   0.0   0.0   1.54087   0.0   0.0
0.0  -0.32012   0.0   0.0   0.0   1.28564   0.0
0.0   0.0;
 0.0   0.0   1.0   0.0   0.0   0.0   0.30768
0.0   0.0   0.0  -0.94000   0.0   0.0   0.0
 -0.76775   0.0;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
1.71704   0.0   0.0   0.0   0.50638   0.0   0.0
0.0   1.41085;
 0.0   0.0   0.0   1.0   0.0   0.0   0.0
0.48385   0.0   0.0   0.0  -0.52675   0.0   0.0
0.0   0.73974;
 1.0   0.0   0.0   0.0  -0.92552   0.0   0.0
0.0   1.53950   0.0   0.0   0.0  -0.76274   0.0
0.0   0.0;
 1.0   0.0   0.0   0.0   0.66002   0.0   0.0
0.0   0.91963   0.0   0.0   0.0  -0.50731   0.0
0.0   0.0;
 0.0   1.0   0.0   0.0   0.0  -0.39700   0.0
0.0   0.0  -0.94000   0.0   0.0   0.0  -0.93803
0.0   0.0;
 1.0   0.0   0.0   0.0  -0.04466   0.0   0.0
0.0   0.29975   0.0   0.0   0.0  -1.07325   0.0
0.0   0.0;
 0.0   1.0   

Re: [Freesurfer] mri_glmfit error

[Greve, Douglas N.,Ph.D.]

Did you see the part where it says "If you seek help with this problem, make 
sure to send:"?

On 9/5/2019 11:00 PM, Gwang-Won Kim wrote:

External Email - Use Caution

Hi there,

I tried to analysed "mri_glmfit --glmdir g1v7.wls --y ces.nii.gz --wls 
cesvar.nii.gz --C Main.mtx --C PDI.mtx --C Sex.mtx --C Age.mtx --C Edu.mtx --C 
BDI.mtx --C SBQ.mtx --C CD.mtx --fsgd g1v7.fsgd --surface fsaverage lh --cortex 
--fwhm 5 "

There were messages for error as follows: Possible problem with experimental 
design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --glmdir g1v7.wls --y ces.nii.gz --wls cesvar.nii.gz --C 
Main.mtx --C PDI.mtx --C Sex.mtx --C Age.mtx --C Edu.mtx --C BDI.mtx --C 
SBQ.mtx --C CD.mtx --fsgd g1v7.fsgd --surface fsaverage lh --cortex --fwhm 5
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=8.774964 (col 3), Max=724.138794 (col 8)
 The scale is much different between columns 3 and 8, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.


What is the problem?

Gwang-Won Kim



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[Freesurfer] mri_glmfit error

[Gwang-Won Kim]

External Email - Use CautionHi there, I tried to analysed "mri_glmfit --glmdir g1v7.wls --y ces.nii.gz --wls cesvar.nii.gz --C Main.mtx --C PDI.mtx --C Sex.mtx --C Age.mtx --C Edu.mtx --C BDI.mtx --C SBQ.mtx --C CD.mtx --fsgd g1v7.fsgd --surface fsaverage lh --cortex --fwhm 5 " There were messages for error as follows:  Possible problem with experimental design:Check for duplicate entries and/or lack of range ofcontinuous variables within a class.If you seek help with this problem, make sure to send:  1. Your command line:    mri_glmfit.bin --glmdir g1v7.wls --y ces.nii.gz --wls cesvar.nii.gz --C Main.mtx --C PDI.mtx --C Sex.mtx --C Age.mtx --C Edu.mtx --C BDI.mtx --C SBQ.mtx --C CD.mtx --fsgd g1v7.fsgd --surface fsaverage lh --cortex --fwhm 5   2. The FSGD file (if using one)  3. And the design matrix aboveAttempting to diagnose further SumSq: Min=8.774964 (col 3), Max=724.138794 (col 8) The scale is much different between columns 3 and 8, you may want to  normalize by subtracting the mean and dividing by the standard deviation.  What is the problem? Gwang-Won Kim













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Re: [Freesurfer] mri_glmfit ERROR no voxels found

[Douglas N. Greve]

There should not be any rounding in mris_preproc, so I don't know why it 
is behaving in that way.


On 06/08/2018 05:12 AM, Marine Boudot de la Motte wrote:
>
>
> Dear Douglas,
>
> Thank you very much for your answer.
> Actually, I looked a little bit deeper into the problem, and found out 
> that when I project the MTR of each subject on the surface, all my MTR 
> values are correct and well projected.
> But once I run mris_preproc to bring everything to fsaverage; all 
> values go to zero.
> I think that this is linked to the fact that all my MTR values are 
> below 0.5 and that there is a round.
> So I tried to run mris_preproc again after multiplying the MTR images 
> for 100; and by doing so the values on fsaverage were correct, but all 
> integer.
> Is there a way to tell mris_preproc to treat the values as float and 
> not to round them?
>
> Thank you again for your kind help.
>
> Marine
>
> 2018-06-06 16:20 GMT+02:00 Douglas Greve  >:
>
> By default, mri_glmfit will exclude any voxels where there is even
> a single data point that is 0. It looks like all your voxels fall
> into that category. If this is really ok and you want to analyze
> voxels where some data points are 0, then add --no-prune.
>
>
> On 6/6/18 4:12 PM, Marine Boudot de la Motte wrote:
>>
>>
>> Hello FreeSurfer Developers,
>>
>> I'm attempting to do a Surface-based analysis on Freesurfer while
>> projecting MTR MRI sequences.
>> I have followed all the steps explained in the group analysis
>> tutorials, and the mri_preproc seems to have ran correctly but
>> once the mri_glmfit is launched i get the following error :
>>
>> Computing normalized matrix
>> Normalized matrix condition is 38.1502
>> Matrix condition is 1.78431e+12
>> Found 149926 points in label.
>> Pruning voxels by thr: 1.175494e-38
>> Found 0 voxels in mask
>> ERROR: no voxels found in the mask
>>   make sure at least one voxel has a non-zero value for each input
>>
>> I've searched the list but didn't find an answer. Does anyone
>> have any clue on how to solve this problem ?
>>
>> Thank you very much for your help,
>>
>> Marine
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> 
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> 
>
>
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> 
>
>
> The information in this e-mail is intended only for the person to
> whom it is
> addressed. If you believe this e-mail was sent to you in error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline
>  . If the e-mail was sent
> to you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
>
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Re: [Freesurfer] mri_glmfit ERROR no voxels found

[Marine Boudot de la Motte]

External Email - Use Caution

Dear Douglas,

Thank you very much for your answer.
Actually, I looked a little bit deeper into the problem, and found out that
when I project the MTR of each subject on the surface, all my MTR values
are correct and well projected.
But once I run mris_preproc to bring everything to fsaverage; all values go
to zero.
I think that this is linked to the fact that all my MTR values are below
0.5 and that there is a round.
So I tried to run mris_preproc again after multiplying the MTR images for
100; and by doing so the values on fsaverage were correct, but all integer.
Is there a way to tell mris_preproc to treat the values as float and not to
round them?

Thank you again for your kind help.

Marine

2018-06-06 16:20 GMT+02:00 Douglas Greve :

> By default, mri_glmfit will exclude any voxels where there is even a
> single data point that is 0. It looks like all your voxels fall into that
> category. If this is really ok and you want to analyze voxels where some
> data points are 0, then add --no-prune.
>
> On 6/6/18 4:12 PM, Marine Boudot de la Motte wrote:
>
>
> Hello FreeSurfer Developers,
>
> I'm attempting to do a Surface-based analysis on Freesurfer while
> projecting MTR MRI sequences.
> I have followed all the steps explained in the group analysis tutorials,
> and the mri_preproc seems to have ran correctly but once the mri_glmfit is
> launched i get the following error :
>
> Computing normalized matrix
> Normalized matrix condition is 38.1502
> Matrix condition is 1.78431e+12
> Found 149926 points in label.
> Pruning voxels by thr: 1.175494e-38
> Found 0 voxels in mask
> ERROR: no voxels found in the mask
>   make sure at least one voxel has a non-zero value for each input
>
> I've searched the list but didn't find an answer. Does anyone have any
> clue on how to solve this problem ?
>
> Thank you very much for your help,
>
> Marine
>
>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_glmfit ERROR no voxels found

[Douglas Greve]

By default, mri_glmfit will exclude any voxels where there is even a 
single data point that is 0. It looks like all your voxels fall into 
that category. If this is really ok and you want to analyze voxels where 
some data points are 0, then add --no-prune.



On 6/6/18 4:12 PM, Marine Boudot de la Motte wrote:



Hello FreeSurfer Developers,

I'm attempting to do a Surface-based analysis on Freesurfer while 
projecting MTR MRI sequences.
I have followed all the steps explained in the group analysis 
tutorials, and the mri_preproc seems to have ran correctly but once 
the mri_glmfit is launched i get the following error :


Computing normalized matrix
Normalized matrix condition is 38.1502
Matrix condition is 1.78431e+12
Found 149926 points in label.
Pruning voxels by thr: 1.175494e-38
Found 0 voxels in mask
ERROR: no voxels found in the mask
  make sure at least one voxel has a non-zero value for each input

I've searched the list but didn't find an answer. Does anyone have any 
clue on how to solve this problem ?


Thank you very much for your help,

Marine




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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] mri_glmfit ERROR no voxels found

[Marine Boudot de la Motte]

External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to do a Surface-based analysis on Freesurfer while
projecting MTR MRI sequences.
I have followed all the steps explained in the group analysis tutorials,
and the mri_preproc seems to have ran correctly but once the mri_glmfit is
launched i get the following error :

Computing normalized matrix
Normalized matrix condition is 38.1502
Matrix condition is 1.78431e+12
Found 149926 points in label.
Pruning voxels by thr: 1.175494e-38
Found 0 voxels in mask
ERROR: no voxels found in the mask
  make sure at least one voxel has a non-zero value for each input

I've searched the list but didn't find an answer. Does anyone have any clue
on how to solve this problem ?

Thank you very much for your help,

Marine
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_glmfit ERROR: loading gamma0

[Douglas Greve]

Can you send me the mtx file?


On 1/11/18 3:08 AM, Gemma Salvadó Blasco wrote:

Hi Douglas,

yes, the file exists and I have read permissions. Is there any file 
(.log, error,...?) that could you help to understand where the problem is?


Thank you,

Gemma

On 10 January 2018 at 00:07, Douglas N Greve 
> wrote:


does this file exist and do you have read permissions?


/home/gsalvado/Projects/Amyloid_Staging/Data/FreeSurfer/Stage0-stage1NoSex.intercept.mtx



On 01/09/2018 09:34 AM, Gemma Salvadó Blasco wrote:
> Hello Freesurfer developers,
> I'm make a statistical analysis between two groups. To do this, I
> followed the instructions of the Fs tutorial
>
(https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
)
> but I'm having a problem at the last step of the process
(mri_glmfit).
> I've checked that all the folders have the same number of
folders and
> documents. Moreover, I've also checked, visually, all the thickness
> images but there is no problem there. However, when I run mri_glmfit
> command in the console appears:
>
> Loading gamma0 file
> MatrixRead( ) - file open failed
>
> No such file or directory
> ERROR: loading gamma0
>
> FreeSurfer
> version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> OS: ubuntu 16.04LTS
>
> I attach mri_glmfit.log
>
> Thank you very much in advance,
>
> Gemma
>
>
> --
> *Gemma Salvadó Blasco
> *Neuroimage PhD Student
> *BarcelonaBeta**Brain Research Center (BBRC)
> *gsalv...@barcelonabeta.org 
>
> T. (+34) 902 33 15 33 
>

>
> C/ Wellington, 30
>

>
> 08005 Barcelona
>

>
> www.barcelonabeta.org 

> www.fpmaragall.org 
/
> /
>
>
>

>
> Aquest missatge i els seus annexos poden contenir informació
> confidencial i exclusiva per al destinatari. El seu contingut no
> constitueix un compromís per part de l'emissor. Si rep aquest
missatge
> per error, si us plau elimini’l sense revisar-lo ni reenviar-lo i
> notifiqui-ho al remitent. Gràcies per la seva col·laboració. /Este
> mensaje y sus anexos pueden contener información confidencial y
> exclusiva para el destinatario. Su contenido no constituye un
> compromiso por parte del emisor. Si recibe este mensaje por
error, por
> favor elimínelo sin revisarlo ni reenviarlo y notifíquelo al
> remitente. //Gracias por su colaboración. /This message and
> attachments may contain confidential and exclusive information
> intended only for the individual named. The content of this message
> does not imply any commitment by the sender. If you have
received this
> e-mail by mistake, please delete it before reading or
distributing and
> notify the sender. Thank you for your cooperation._
> _Gràcies per estalviar paper. /Gracias por ahorrar papel.
/Thanks for
> saving paper.
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu

> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358 
Fax: 617-726-7422 

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2

www.nmr.mgh.harvard.edu/facility/filedrop/index.html

Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

Re: [Freesurfer] mri_glmfit ERROR: loading gamma0

[Gemma Salvadó Blasco]

Hi Douglas,

yes, the file exists and I have read permissions. Is there any file (.log,
error,...?) that could you help to understand where the problem is?

Thank you,

Gemma

On 10 January 2018 at 00:07, Douglas N Greve 
wrote:

> does this file exist and do you have read permissions?
>
> /home/gsalvado/Projects/Amyloid_Staging/Data/
> FreeSurfer/Stage0-stage1NoSex.intercept.mtx
>
>
>
> On 01/09/2018 09:34 AM, Gemma Salvadó Blasco wrote:
> > Hello Freesurfer developers,
> > I'm make a statistical analysis between two groups. To do this, I
> > followed the instructions of the Fs tutorial
> > (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis)
> > but I'm having a problem at the last step of the process (mri_glmfit).
> > I've checked that all the folders have the same number of folders and
> > documents. Moreover, I've also checked, visually, all the thickness
> > images but there is no problem there. However, when I run mri_glmfit
> > command in the console appears:
> >
> > Loading gamma0 file
> > MatrixRead( ) - file open failed
> >
> > No such file or directory
> > ERROR: loading gamma0
> >
> > FreeSurfer
> > version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> > OS: ubuntu 16.04LTS
> >
> > I attach mri_glmfit.log
> >
> > Thank you very much in advance,
> >
> > Gemma
> >
> >
> > --
> > *Gemma Salvadó Blasco
> > *Neuroimage PhD Student
> > *BarcelonaBeta**Brain Research Center (BBRC)
> > *gsalv...@barcelonabeta.org 
> > T. (+34) 902 33 15 33
> >  fs=fundacio+pasqual+maragall=utf-8=utf-8#>
> > C/ Wellington, 30
> >  Barcelona=gmail=g>
> > 08005 Barcelona
> >  Barcelona=gmail=g>
> > www.barcelonabeta.org 
> > www.fpmaragall.org /
> > /
> >
> >
> > 
> >
> > Aquest missatge i els seus annexos poden contenir informació
> > confidencial i exclusiva per al destinatari. El seu contingut no
> > constitueix un compromís per part de l'emissor. Si rep aquest missatge
> > per error, si us plau elimini’l sense revisar-lo ni reenviar-lo i
> > notifiqui-ho al remitent. Gràcies per la seva col·laboració. /Este
> > mensaje y sus anexos pueden contener información confidencial y
> > exclusiva para el destinatario. Su contenido no constituye un
> > compromiso por parte del emisor. Si recibe este mensaje por error, por
> > favor elimínelo sin revisarlo ni reenviarlo y notifíquelo al
> > remitente. //Gracias por su colaboración. /This message and
> > attachments may contain confidential and exclusive information
> > intended only for the individual named. The content of this message
> > does not imply any commitment by the sender. If you have received this
> > e-mail by mistake, please delete it before reading or distributing and
> > notify the sender. Thank you for your cooperation._
> > _Gràcies per estalviar paper. /Gracias por ahorrar papel. /Thanks for
> > saving paper.
> >
> >
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> ___
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> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
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-- 

*Gemma Salvadó Blasco*Neuroimage PhD Student
*BarcelonaBeta*
* Brain Research Center (BBRC) *gsalv...@barcelonabeta.org

T. (+34) 902 33 15 33

C/ Wellington, 30

08005 Barcelona

www.barcelonabeta.org
www.fpmaragall.org


--

Aquest missatge i els seus annexos poden contenir informació confidencial i
exclusiva per al destinatari. El seu contingut 

Re: [Freesurfer] mri_glmfit ERROR: loading gamma0

[Douglas N Greve]

does this file exist and do you have read permissions?

/home/gsalvado/Projects/Amyloid_Staging/Data/FreeSurfer/Stage0-stage1NoSex.intercept.mtx
 



On 01/09/2018 09:34 AM, Gemma Salvadó Blasco wrote:
> Hello Freesurfer developers,
> I'm make a statistical analysis between two groups. To do this, I 
> followed the instructions of the Fs tutorial 
> (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) 
> but I'm having a problem at the last step of the process (mri_glmfit). 
> I've checked that all the folders have the same number of folders and 
> documents. Moreover, I've also checked, visually, all the thickness 
> images but there is no problem there. However, when I run mri_glmfit 
> command in the console appears:
>
> Loading gamma0 file
> MatrixRead( ) - file open failed
>
> No such file or directory
> ERROR: loading gamma0
>
> FreeSurfer 
> version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> OS: ubuntu 16.04LTS
>
> I attach mri_glmfit.log
>
> Thank you very much in advance,
>
> Gemma
>
>
> -- 
> *Gemma Salvadó Blasco
> *Neuroimage PhD Student
> *BarcelonaBeta**Brain Research Center (BBRC)
> *gsalv...@barcelonabeta.org 
> T. (+34) 902 33 15 33 
> 
> C/ Wellington, 30 
> 
> 08005 Barcelona 
> 
> www.barcelonabeta.org 
> www.fpmaragall.org /
> /
>
>
> 
>
> Aquest missatge i els seus annexos poden contenir informació 
> confidencial i exclusiva per al destinatari. El seu contingut no 
> constitueix un compromís per part de l'emissor. Si rep aquest missatge 
> per error, si us plau elimini’l sense revisar-lo ni reenviar-lo i 
> notifiqui-ho al remitent. Gràcies per la seva col·laboració. /Este 
> mensaje y sus anexos pueden contener información confidencial y 
> exclusiva para el destinatario. Su contenido no constituye un 
> compromiso por parte del emisor. Si recibe este mensaje por error, por 
> favor elimínelo sin revisarlo ni reenviarlo y notifíquelo al 
> remitente. //Gracias por su colaboración. /This message and 
> attachments may contain confidential and exclusive information 
> intended only for the individual named. The content of this message 
> does not imply any commitment by the sender. If you have received this 
> e-mail by mistake, please delete it before reading or distributing and 
> notify the sender. Thank you for your cooperation._
> _Gràcies per estalviar paper. /Gracias por ahorrar papel. /Thanks for 
> saving paper.
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] mri_glmfit ERROR: loading gamma0

[Gemma Salvadó Blasco]

Hello Freesurfer developers,
I'm make a statistical analysis between two groups. To do this, I followed
the instructions of the Fs tutorial (
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) but I'm
having a problem at the last step of the process (mri_glmfit). I've checked
that all the folders have the same number of folders and documents.
Moreover, I've also checked, visually, all the thickness images but there
is no problem there. However, when I run mri_glmfit command in the console
appears:

Loading gamma0 file
MatrixRead( ) - file open failed

No such file or directory
ERROR: loading gamma0

FreeSurfer version:freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
OS: ubuntu 16.04LTS

I attach mri_glmfit.log

Thank you very much in advance,

Gemma


-- 

*Gemma Salvadó Blasco*Neuroimage PhD Student
*BarcelonaBeta*
* Brain Research Center (BBRC) *gsalv...@barcelonabeta.org

T. (+34) 902 33 15 33

C/ Wellington, 30

08005 Barcelona

www.barcelonabeta.org
www.fpmaragall.org


--

Aquest missatge i els seus annexos poden contenir informació confidencial i
exclusiva per al destinatari. El seu contingut no constitueix un compromís
per part de l'emissor. Si rep aquest missatge per error, si us plau
elimini’l sense revisar-lo ni reenviar-lo i notifiqui-ho al remitent.
Gràcies per la seva col·laboració. *Este mensaje y sus anexos pueden
contener información confidencial y exclusiva para el destinatario. Su
contenido no constituye un compromiso por parte del emisor. Si recibe este
mensaje por error, por favor elimínelo sin revisarlo ni reenviarlo y
notifíquelo al remitente. **Gracias por su colaboración. *This message and
attachments may contain confidential and exclusive information intended
only for the individual named. The content of this message does not imply
any commitment by the sender. If you have received this e-mail by mistake,
please delete it before reading or distributing and notify the sender.
Thank you for your cooperation.
Gràcies per estalviar paper. *Gracias por ahorrar papel. *Thanks for saving
paper.

$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
cwd /home/gsalvado/Projects/Freesurfer_prova/Prova_thickness
cmdline mri_glmfit.bin --glmdir /home/gsalvado/Projects/Freesurfer_prova/Prova_thickness/GLM/ --y /home/gsalvado/Projects/Freesurfer_prova/Prova_thickness/lh.ProvaStage.thickness.5B.mgh --surf fsaverage lh --fsgd /home/gsalvado/Projects/Amyloid_Staging/Data/FreeSurfer/FGSD/ProvaStage.fsgd dods --C /home/gsalvado/Projects/Amyloid_Staging/Data/FreeSurfer/Stage0-stage1NoSex.intercept.mtx   
sysname  Linux
hostname WS128012
machine  x86_64
user gsalvado
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/home/gsalvado/Projects/Freesurfer_prova/Prova_thickness/lh.ProvaStage.thickness.5B.mgh
logyflag 0
usedti  0
FSGD /home/gsalvado/Projects/Amyloid_Staging/Data/FreeSurfer/FGSD/ProvaStage.fsgd
labelmask  /home/gsalvado/Projects/Freesurfer_prova/fsaverage/label/lh.cortex.label
maskinv 0
glmdir /home/gsalvado/Projects/Freesurfer_prova/Prova_thickness/GLM/
IllCondOK 0
ReScaleX 1
DoFFx 0
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Re: [Freesurfer] mri_glmfit error (mri_reshape number of elements)

[Douglas Greve]

not sure what is going wrong. Does it work if you do not include the 
--wls cesvar.nii.gz ?



On 6/28/17 12:29 PM, Mcnorgan, Christopher wrote:

Hi,
I’m running a group-level analysis and have encountered an error that 
results in a core dump. The first-level analyses were run using the 
fsaverage surfaces, rather than self surfaces. I’ve already inspected 
the individual contrasts, loading the fsaverage surface in tksurfer 
and rendering each subject’s contrast as an overlay, and would now 
like to compute the group-level results.


I first ran isxconcat-sess, and saw no errors indicated in the program 
output.


mri_glmfit was then called as followed, and produced the following 
output (same result for the rh):


$ mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surf
fsaverage lh --glmdir glm.wls --nii.gz
Reading source surface /home/chris/LDT/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces  327680
Total area 65416.648438
AvgVtxArea 0.399267
AvgVtxDist 0.721953
StdVtxDist 0.195470

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo
cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm
--surf fsaverage lh --glmdir glm.wls --nii.gz
sysname  Linux
hostname brocasarea
machine  x86_64
user chris
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 1
y  /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo/ces.nii.gz
logyflag 0
usedti  0
labelmask  /home/chris/LDT/fsaverage/label/lh.cortex.label
maskinv 0
glmdir glm.wls
IllCondOK 0
ReScaleX 1
DoFFx 0
wFile cesvar.nii.gz
weightinv  1
weightsqrt 1
Creating output directory glm.wls
Loading y from
/home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo/ces.nii.gz
Saving design matrix to glm.wls/Xg.dat
Normalized matrix condition is 1
Matrix condition is 1
Found 149955 points in label.
ERROR: mri_reshape: number of elements cannot change
  nv1 = 163842, nv1 = 537168
Pruning voxels by thr: 0.00
Segmentation fault (core dumped)


This seems to have its root in a mismatch between the vertices in the 
fsaverage lh.cortex label and those in the contrast data. However, I 
carried out subject-level analyses in the fsaverage surface space 
specifically to facilitate a group-level analysis in fsaverage surface 
space, so I can’t see where I went wrong. The only other post I could 
find that was similar was related to an attempt to carry out a group 
analysis in native surface space, which is not the case here.


Thanks for your time



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[Freesurfer] mri_glmfit error (mri_reshape number of elements)

[Mcnorgan, Christopher]

Hi,
I’m running a group-level analysis and have encountered an error that results 
in a core dump. The first-level analyses were run using the fsaverage surfaces, 
rather than self surfaces. I’ve already inspected the individual contrasts, 
loading the fsaverage surface in tksurfer and rendering each subject’s contrast 
as an overlay, and would now like to compute the group-level results.

I first ran isxconcat-sess, and saw no errors indicated in the program output.

mri_glmfit was then called as followed, and produced the following output (same 
result for the rh):

$ mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surf fsaverage lh 
--glmdir glm.wls --nii.gz
Reading source surface /home/chris/LDT/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces327680
Total area 65416.648438
AvgVtxArea   0.399267
AvgVtxDist   0.721953
StdVtxDist   0.195470

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo
cmdline mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surf fsaverage 
lh --glmdir glm.wls --nii.gz
sysname  Linux
hostname brocasarea
machine  x86_64
user chris
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 1
y/home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo/ces.nii.gz
logyflag 0
usedti  0
labelmask  /home/chris/LDT/fsaverage/label/lh.cortex.label
maskinv 0
glmdir glm.wls
IllCondOK 0
ReScaleX 1
DoFFx 0
wFile cesvar.nii.gz
weightinv  1
weightsqrt 1
Creating output directory glm.wls
Loading y from /home/chris/LDT/RFX/LDT_fsaverage.sm4.rh/hi-v-lo/ces.nii.gz
Saving design matrix to glm.wls/Xg.dat
Normalized matrix condition is 1
Matrix condition is 1
Found 149955 points in label.
ERROR: mri_reshape: number of elements cannot change
  nv1 = 163842, nv1 = 537168
Pruning voxels by thr: 0.00
Segmentation fault (core dumped)

This seems to have its root in a mismatch between the vertices in the fsaverage 
lh.cortex label and those in the contrast data. However, I carried out 
subject-level analyses in the fsaverage surface space specifically to 
facilitate a group-level analysis in fsaverage surface space, so I can’t see 
where I went wrong. The only other post I could find that was similar was 
related to an attempt to carry out a group analysis in native surface space, 
which is not the case here.

Thanks for your time

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Re: [Freesurfer] mri_glmfit error with aparc table flag

[Douglas N Greve]

t; > > > <mailto:miracoo...@gmail.com
> <mailto:miracoo...@gmail.com>
> > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>>
> <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>
> > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>>>>
> > > > > <mailto:miracoo...@gmail.com
> <mailto:miracoo...@gmail.com>
> > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>>
> <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>
> > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>>>
> > > <mailto:miracoo...@gmail.com
> <mailto:miracoo...@gmail.com> <mailto:miracoo...@gmail.com
> <mailto:miracoo...@gmail.com>>
> > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>
> <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>>>>> wrote:
> > > > >> Thanks doug. Does it mean when using the
> --table
> > > flag, you
> > > > can't
> > > > >> use the fsaverage template? I came across
> several
> > > post in the
> > > > >> forum that used "--surf fsaverage lh "‎
> and it
> > worked.
> > > > >> Best,
> > > > >> Paul
> > > > >>
> > > > >> Sent from my BlackBerry 10 smartphone.
> > > > >> *From: *Douglas Greve
> > > > >> *Sent: *Tuesday, April 18, 2017 9:52 PM
> > > > >> *To: *freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > > > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>>
> > > > >> <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > > > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>>>
> > > > >> *Reply To: *Freesurfer support list
> > > > >> *Subject: *Re: [Freesurfer] mri_glmfit error
> > with aparc
> > > > table flag
> > > > >>
> > > > >>
> > > > >> Don't include --surf fsaverage lh. It
> thinks the
> > > input is a
> > > > >> surface, not a table
> > > > >>
> > > > >>
> > > > >>
> > > > >> On 4/18/17 9:21 PM, miracle ozzoude wrote:
> > > > >>> Hello freesurfer,
> > > > >>> I am trying to run mri_glmfit with the
> --table
> 

Re: [Freesurfer] mri_glmfit error with aparc table flag

[miracle ozzoude]

   file.
> > > > > Also, I was trying to visualize the result on the
> > surface
> > > using
> > > > > freeview -f fsaverage/lh.pial -viewport 3d (clicking
> > > overlay on
> > > > > freeview and loading the sig.mgh). However, i got an
> > error "
> > > > failed to
> > > > > display overlay". How can I visualize the result?
> Thanks
> > > > > Best,
> > > > > Paul
> > > > >
> > > > > On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve
> > > > > <gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu
> >>>
> > > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>
> > > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>>>> wrote:
> > > > >
> > > > > You have a table of data, so no template is
> > needed. If you
> > > > put the
> > > > > --surf before the --table, it probably runs, but it
> > > will ignore
> > > > > the surface
> > > > >
> > > > >
> > > > > On 4/18/17 9:58 PM, miracoo...@gmail.com
> > <mailto:miracoo...@gmail.com>
> > > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>>
> > > > <mailto:miracoo...@gmail.com
> > <mailto:miracoo...@gmail.com> <mailto:miracoo...@gmail.com
> > <mailto:miracoo...@gmail.com>>>
> > > > > <mailto:miracoo...@gmail.com
> > <mailto:miracoo...@gmail.com> <mailto:miracoo...@gmail.com
> > <mailto:miracoo...@gmail.com>>
> > > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>
> > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>>>> wrote:
> > > > >> Thanks doug. Does it mean when using the --table
> > > flag, you
> > > > can't
> > > > >> use the fsaverage template? I came across several
> > > post in the
> > > > >> forum that used "--surf fsaverage lh "‎ and it
> > worked.
> > > > >> Best,
> > > > >> Paul
> > > > >>
> > > > >> Sent from my BlackBerry 10 smartphone.
> > > > >> *From: *Douglas Greve
> > > > >> *Sent: *Tuesday, April 18, 2017 9:52 PM
> > > > >> *To: *freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > > <mailto:freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > > > >> <mailto:freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > > <mailto:freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>>>>
> > > > >> *Reply To: *Freesurfer support list
> > > > >> *Subject: *Re

Re: [Freesurfer] mri_glmfit error with aparc table flag

[Douglas N Greve]

.edu>>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>>>> wrote:
> > > >
> > > > You have a table of data, so no template is
> needed. If you
> > > put the
> > > > --surf before the --table, it probably runs, but it
> > will ignore
> > > > the surface
> > > >
> > > >
> > > > On 4/18/17 9:58 PM, miracoo...@gmail.com
> <mailto:miracoo...@gmail.com>
> > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>>
> > > <mailto:miracoo...@gmail.com
> <mailto:miracoo...@gmail.com> <mailto:miracoo...@gmail.com
> <mailto:miracoo...@gmail.com>>>
> > > > <mailto:miracoo...@gmail.com
> <mailto:miracoo...@gmail.com> <mailto:miracoo...@gmail.com
> <mailto:miracoo...@gmail.com>>
> > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>
> <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>>>> wrote:
> > > >> Thanks doug. Does it mean when using the --table
> > flag, you
> > > can't
> > > >> use the fsaverage template? I came across several
> > post in the
> > > >> forum that used "--surf fsaverage lh "‎ and it
> worked.
> > > >> Best,
> > > >> Paul
> > > >>
> > > >> Sent from my BlackBerry 10 smartphone.
> > > >> *From: *Douglas Greve
> > > >> *Sent: *Tuesday, April 18, 2017 9:52 PM
> > > >> *To: *freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > > >> <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>>
> > > >> *Reply To: *Freesurfer support list
> > > >> *Subject: *Re: [Freesurfer] mri_glmfit error
> with aparc
> > > table flag
> > > >>
> > > >>
> > > >> Don't include --surf fsaverage lh. It thinks the
> > input is a
> > > >> surface, not a table
> > > >>
> > > >>
> > > >>
> > > >> On 4/18/17 9:21 PM, miracle ozzoude wrote:
> > > >>> Hello freesurfer,
> > > >>> I am trying to run mri_glmfit with the --table
> flag. My
> > > >>>  aparc_lh_thick_stats.txt contain entorhinal and
> > > parahippocampal
> > > >>> thickness values for 32 subjects. I ran the glm
> > command and
> > > >>> received an error. Please, how can i solve this
> > issue? I have
> > > >>> included my command, fsgd file, contrast
> matrix and
> > error
> > > below.
> > > >>> Thanks
> > > >>> Best,
> > > >>> Paul
> > > >>>
> > > >>> GLM command: mri_glmfit --table
> aparc_lh_thick_stats.txt
> > > --fsgd
> > > >>> age.fsgd --C age1.mtx --C age2.mtx --surf
> fsaverage lh
> > > --cortex
&g

Re: [Freesurfer] mri_glmfit error with aparc table flag

[miracle ozzoude]

Hello Doug,
I downloaded and installed octave. However, I can't find the
annotval2surfoverlay.m
file in the matlab directory of freesurfer. Does it come with FS v6 or do i
need to download the file? Also, I was looking into the
annotval2surfoverlay file and I have couple of questions.
% Run these commands in matlab
% annotnames = strvcat('superiortemporal','insula','postcentral');
% annotvals = [1.1 2.2 3.7];
% annotfile = '~/subjects/fsaverage/label/lh.aparc.annot';
% surfoverlay = annotval2surfoverlay(annotvals,annotnames,annotfile);
% clear mri
% mri.vol = surfoverlay;
% MRIwrite(mri,'vals.mgh');
%
1) Are the annotation values (annotvals) from results after correcting for
multiple comparisons using mri_fdr?
2) Do I need to add octave path to freesurfer PATH like the example below?

setenv FS_USE_OCTAVE 4.0.3

setenv FS_OCTAVE_LIB /Applications/octave/lib
setenv FS_OCTAVE_BIN /Application/octave/binary


On Wed, Apr 19, 2017 at 3:39 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> I think that will work
>
>
> On 04/19/2017 03:33 PM, miracle ozzoude wrote:
> > Hello Doug,
> > Do you think writing the script with octave can substitute for matlab?
> > I am using FS v6.0 and I have the annotval2surfoverlay.m. Thanks
> > Best,
> > Paul
> >
> > On Wed, Apr 19, 2017 at 1:47 PM, Douglas N Greve
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > Sorry, I don't have another solution for you.
> >
> >
> > On 04/19/2017 01:42 PM, miracle ozzoude wrote:
> > > Thanks Doug. However, I am running freesurfer analysis on my
> > personal
> > > computer and I don't have matlab. Also, I don't know how this
> matlab
> > > script works/ matlab works. Any instructions on how to use it or
> > > alternate? Please and thank you.
> > > Best,
> > > Paul.
> > >
> > > On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve
> > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
> > >
> > > It is a table of data, so you can't visualize it directly on
> > anything.
> > > You can try using annotval2surfoverlay.m to create a surface
> > > overlay of
> > > the data.
> > >
> > >
> > > On 04/19/2017 10:05 AM, miracle ozzoude wrote:
> > > > Hello Doug,
> > > > It worked. The issue was due to formatting error with the
> > aparc
> > > file.
> > > > Also, I was trying to visualize the result on the surface
> > using
> > > > freeview -f fsaverage/lh.pial -viewport 3d (clicking
> > overlay on
> > > > freeview and loading the sig.mgh). However, i got an error "
> > > failed to
> > > > display overlay". How can I visualize the result? Thanks
> > > > Best,
> > > > Paul
> > > >
> > > > On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve
> > > > <gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu
> >>
> > > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>
> > > <mailto:gr...@nmr.mgh.harvard.edu  gr...@nmr.mgh.harvard.edu>>>> wrote:
> > > >
> > > > You have a table of data, so no template is needed. If
> you
> > > put the
> > > > --surf before the --table, it probably runs, but it
> > will ignore
> > > > the surface
> > > >
> > > >
> > > > On 4/18/17 9:58 PM, miracoo...@gmail.com
> > <mailto:miracoo...@gmail.com>
> > > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>>
> > > > <mailto:miracoo...@gmail.com  miracoo...@gmail.com>
> > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>>> wrote:
> > > >> Thanks doug. Does it mean when using the --table
> > flag, you
> > > can't
> > > >> use the fsaverage template? I came across several
> > post in the
> > > >>     forum that used "--sur

Re: [Freesurfer] mri_glmfit error with aparc table flag

[Douglas N Greve]

I think that will work


On 04/19/2017 03:33 PM, miracle ozzoude wrote:
> Hello Doug,
> Do you think writing the script with octave can substitute for matlab? 
> I am using FS v6.0 and I have the annotval2surfoverlay.m. Thanks
> Best,
> Paul
>
> On Wed, Apr 19, 2017 at 1:47 PM, Douglas N Greve 
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Sorry, I don't have another solution for you.
>
>
> On 04/19/2017 01:42 PM, miracle ozzoude wrote:
> > Thanks Doug. However, I am running freesurfer analysis on my
> personal
> > computer and I don't have matlab. Also, I don't know how this matlab
> > script works/ matlab works. Any instructions on how to use it or
> > alternate? Please and thank you.
> > Best,
> > Paul.
> >
> > On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
> >
> > It is a table of data, so you can't visualize it directly on
> anything.
> > You can try using annotval2surfoverlay.m to create a surface
> > overlay of
> > the data.
> >
> >
> > On 04/19/2017 10:05 AM, miracle ozzoude wrote:
> > > Hello Doug,
> > > It worked. The issue was due to formatting error with the
> aparc
> > file.
> > > Also, I was trying to visualize the result on the surface
> using
> > > freeview -f fsaverage/lh.pial -viewport 3d (clicking
> overlay on
> > > freeview and loading the sig.mgh). However, i got an error "
> > failed to
> > > display overlay". How can I visualize the result? Thanks
> > > Best,
> > > Paul
> > >
> > > On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve
> > > <gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>
> > <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu 
> <mailto:gr...@nmr.mgh.harvard.edu>>>> wrote:
> > >
> > > You have a table of data, so no template is needed. If you
> > put the
> > > --surf before the --table, it probably runs, but it
> will ignore
> > > the surface
> > >
> > >
> > > On 4/18/17 9:58 PM, miracoo...@gmail.com
> <mailto:miracoo...@gmail.com>
> > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>>
> > > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>
> <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>>> wrote:
> > >> Thanks doug. Does it mean when using the --table
> flag, you
> > can't
> > >> use the fsaverage template? I came across several
> post in the
> > >> forum that used "--surf fsaverage lh "‎ and it worked.
> > >> Best,
> > >> Paul
> > >>
> > >> Sent from my BlackBerry 10 smartphone.
> > >> *From: *Douglas Greve
> > >> *Sent: *Tuesday, April 18, 2017 9:52 PM
> > >> *To: *freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > >> <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> > <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>>
> > >> *Reply To: *Freesurfer support list
> > >> *Subject: *Re: [Freesurfer] mri_glmfit error with aparc
> > table flag
> > >>
> > >>
> > >> Don't include --surf fsaverage lh. It thinks the
> input is a
> > >> surface, not a table
> > >>
> > >>
> > >>
> > >> On 4/18/17 9:21 PM, miracle ozzoude wrote:
> > >>

Re: [Freesurfer] mri_glmfit error with aparc table flag

[miracle ozzoude]

Hello Doug,
Do you think writing the script with octave can substitute for matlab? I am
using FS v6.0 and I have the annotval2surfoverlay.m. Thanks
Best,
Paul

On Wed, Apr 19, 2017 at 1:47 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> Sorry, I don't have another solution for you.
>
>
> On 04/19/2017 01:42 PM, miracle ozzoude wrote:
> > Thanks Doug. However, I am running freesurfer analysis on my personal
> > computer and I don't have matlab. Also, I don't know how this matlab
> > script works/ matlab works. Any instructions on how to use it or
> > alternate? Please and thank you.
> > Best,
> > Paul.
> >
> > On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > It is a table of data, so you can't visualize it directly on
> anything.
> > You can try using annotval2surfoverlay.m to create a surface
> > overlay of
> > the data.
> >
> >
> > On 04/19/2017 10:05 AM, miracle ozzoude wrote:
> > > Hello Doug,
> > > It worked. The issue was due to formatting error with the aparc
> > file.
> > > Also, I was trying to visualize the result on the surface using
> > > freeview -f fsaverage/lh.pial -viewport 3d (clicking overlay on
> > > freeview and loading the sig.mgh). However, i got an error "
> > failed to
> > > display overlay". How can I visualize the result? Thanks
> > > Best,
> > > Paul
> > >
> > > On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve
> > > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> > <mailto:gr...@nmr.mgh.harvard.edu
> > <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
> > >
> > > You have a table of data, so no template is needed. If you
> > put the
> > > --surf before the --table, it probably runs, but it will ignore
> > > the surface
> > >
> > >
> > > On 4/18/17 9:58 PM, miracoo...@gmail.com
> > <mailto:miracoo...@gmail.com>
> > > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>>
> wrote:
> > >> Thanks doug. Does it mean when using the --table flag, you
> > can't
> > >> use the fsaverage template? I came across several post in the
> > >> forum that used "--surf fsaverage lh "‎ and it worked.
> > >> Best,
> >     >>     Paul
> > >>
> > >> Sent from my BlackBerry 10 smartphone.
> > >> *From: *Douglas Greve
> > >> *Sent: *Tuesday, April 18, 2017 9:52 PM
> > >> *To: *freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>
> > >> <mailto:freesurfer@nmr.mgh.harvard.edu
> > <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > >> *Reply To: *Freesurfer support list
> > >> *Subject: *Re: [Freesurfer] mri_glmfit error with aparc
> > table flag
> > >>
> > >>
> > >> Don't include --surf fsaverage lh. It thinks the input is a
> > >> surface, not a table
> > >>
> > >>
> > >>
> > >> On 4/18/17 9:21 PM, miracle ozzoude wrote:
> > >>> Hello freesurfer,
> > >>> I am trying to run mri_glmfit with the --table flag. My
> > >>> aparc_lh_thick_stats.txt contain entorhinal and
> > parahippocampal
> > >>> thickness values for 32 subjects. I ran the glm command and
> > >>> received an error. Please, how can i solve this issue? I have
> > >>> included my command, fsgd file, contrast matrix and error
> > below.
> > >>> Thanks
> > >>> Best,
> > >>> Paul
> > >>>
> > >>> GLM command: mri_glmfit --table aparc_lh_thick_stats.txt
> > --fsgd
> > >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh
> > --cortex
> > >>> --glmdir lh.thickness.glmdir
> > >>>
> > >>>
> > >>> ERROR= "gdfRead(): reading age.fsgd
> > >>>
> > >>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT b

Re: [Freesurfer] mri_glmfit error with aparc table flag

[Douglas N Greve]

Sorry, I don't have another solution for you.


On 04/19/2017 01:42 PM, miracle ozzoude wrote:
> Thanks Doug. However, I am running freesurfer analysis on my personal 
> computer and I don't have matlab. Also, I don't know how this matlab 
> script works/ matlab works. Any instructions on how to use it or 
> alternate? Please and thank you.
> Best,
> Paul.
>
> On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve 
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> It is a table of data, so you can't visualize it directly on anything.
> You can try using annotval2surfoverlay.m to create a surface
> overlay of
> the data.
>
>
> On 04/19/2017 10:05 AM, miracle ozzoude wrote:
> > Hello Doug,
> > It worked. The issue was due to formatting error with the aparc
> file.
> > Also, I was trying to visualize the result on the surface using
> > freeview -f fsaverage/lh.pial -viewport 3d (clicking overlay on
> > freeview and loading the sig.mgh). However, i got an error "
> failed to
> > display overlay". How can I visualize the result? Thanks
> > Best,
> > Paul
> >
> > On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote:
> >
> > You have a table of data, so no template is needed. If you
> put the
> > --surf before the --table, it probably runs, but it will ignore
> > the surface
> >
> >
> > On 4/18/17 9:58 PM, miracoo...@gmail.com
> <mailto:miracoo...@gmail.com>
> > <mailto:miracoo...@gmail.com <mailto:miracoo...@gmail.com>> wrote:
> >> Thanks doug. Does it mean when using the --table flag, you
> can't
> >> use the fsaverage template? I came across several post in the
> >> forum that used "--surf fsaverage lh "‎ and it worked.
> >> Best,
> >> Paul
> >>
> >> Sent from my BlackBerry 10 smartphone.
> >> *From: *Douglas Greve
>     >> *Sent: *Tuesday, April 18, 2017 9:52 PM
> >> *To: *freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>
> >> <mailto:freesurfer@nmr.mgh.harvard.edu
> <mailto:freesurfer@nmr.mgh.harvard.edu>>
> >> *Reply To: *Freesurfer support list
> >> *Subject: *Re: [Freesurfer] mri_glmfit error with aparc
> table flag
> >>
> >>
> >> Don't include --surf fsaverage lh. It thinks the input is a
> >> surface, not a table
> >>
> >>
> >>
> >> On 4/18/17 9:21 PM, miracle ozzoude wrote:
> >>> Hello freesurfer,
> >>> I am trying to run mri_glmfit with the --table flag. My
> >>> aparc_lh_thick_stats.txt contain entorhinal and
> parahippocampal
> >>> thickness values for 32 subjects. I ran the glm command and
> >>> received an error. Please, how can i solve this issue? I have
> >>> included my command, fsgd file, contrast matrix and error
> below.
> >>> Thanks
> >>> Best,
> >>> Paul
> >>>
> >>> GLM command: mri_glmfit --table aparc_lh_thick_stats.txt
> --fsgd
> >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh
> --cortex
> >>> --glmdir lh.thickness.glmdir
> >>>
> >>>
> >>> ERROR= "gdfRead(): reading age.fsgd
> >>>
> >>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be
> done.
> >>>
> >>> Continuous Variable Means (all subjects)
> >>>
> >>> 0 Age 39.9375 17.3312
> >>>
> >>> Class Means of each Continuous Variable
> >>>
> >>> 1 Group1  35.6316
> >>>
> >>> 2 Group2  46.2308
> >>>
> >>> INFO: gd2mtx_method is dods
> >>>
> >>> Reading source surface
> >>>   
>  /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white
> >>>
> >>> Number of vertices 163842
&

Re: [Freesurfer] mri_glmfit error with aparc table flag

[miracle ozzoude]

Thanks Doug. However, I am running freesurfer analysis on my personal
computer and I don't have matlab. Also, I don't know how this matlab script
works/ matlab works. Any instructions on how to use it or alternate? Please
and thank you.
Best,
Paul.

On Wed, Apr 19, 2017 at 1:33 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> It is a table of data, so you can't visualize it directly on anything.
> You can try using annotval2surfoverlay.m to create a surface overlay of
> the data.
>
>
> On 04/19/2017 10:05 AM, miracle ozzoude wrote:
> > Hello Doug,
> > It worked. The issue was due to formatting error with the aparc file.
> > Also, I was trying to visualize the result on the surface using
> > freeview -f fsaverage/lh.pial -viewport 3d (clicking overlay on
> > freeview and loading the sig.mgh). However, i got an error " failed to
> > display overlay". How can I visualize the result? Thanks
> > Best,
> > Paul
> >
> > On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve
> > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
> >
> > You have a table of data, so no template is needed. If you put the
> > --surf before the --table, it probably runs, but it will ignore
> > the surface
> >
> >
> > On 4/18/17 9:58 PM, miracoo...@gmail.com
> > <mailto:miracoo...@gmail.com> wrote:
> >> Thanks doug. Does it mean when using the --table flag, you can't
> >> use the fsaverage template? I came across several post in the
> >> forum that used "--surf fsaverage lh "‎ and it worked.
> >> Best,
> >> Paul
> >>
> >> Sent from my BlackBerry 10 smartphone.
> >>     *From: *Douglas Greve
> >> *Sent: *Tuesday, April 18, 2017 9:52 PM
> >> *To: *freesurfer@nmr.mgh.harvard.edu
> >> <mailto:freesurfer@nmr.mgh.harvard.edu>
> >> *Reply To: *Freesurfer support list
> >> *Subject: *Re: [Freesurfer] mri_glmfit error with aparc table flag
> >>
> >>
> >> Don't include --surf fsaverage lh. It thinks the input is a
> >> surface, not a table
> >>
> >>
> >>
> >> On 4/18/17 9:21 PM, miracle ozzoude wrote:
> >>> Hello freesurfer,
> >>> I am trying to run mri_glmfit with the --table flag. My
> >>> aparc_lh_thick_stats.txt contain entorhinal and parahippocampal
> >>> thickness values for 32 subjects. I ran the glm command and
> >>> received an error. Please, how can i solve this issue? I have
> >>> included my command, fsgd file, contrast matrix and error below.
> >>> Thanks
> >>> Best,
> >>> Paul
> >>>
> >>> GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd
> >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex
> >>> --glmdir lh.thickness.glmdir
> >>>
> >>>
> >>> ERROR= "gdfRead(): reading age.fsgd
> >>>
> >>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> >>>
> >>> Continuous Variable Means (all subjects)
> >>>
> >>> 0 Age 39.9375 17.3312
> >>>
> >>> Class Means of each Continuous Variable
> >>>
> >>> 1 Group1  35.6316
> >>>
> >>> 2 Group2  46.2308
> >>>
> >>> INFO: gd2mtx_method is dods
> >>>
> >>> Reading source surface
> >>> /Users/MiracleOz/Documents/improvervsdeclinermri/
> fsaverage/surf/lh.white
> >>>
> >>> Number of vertices 163842
> >>>
> >>> Number of faces327680
> >>>
> >>> Total area 65416.984375
> >>>
> >>> AvgVtxArea   0.399269
> >>>
> >>> AvgVtxDist   0.721953
> >>>
> >>> StdVtxDist   0.195470
> >>>
> >>>
> >>> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
> >>>
> >>> cwd /Users/MiracleOz/Documents/improvervsdeclinermri
> >>>
> >>> cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd
> >>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex
> >>> --glmdir lh.thickness.glmdir
> >>>
> >>> sysname Darwin
> >>>
> >>> hostname MacBook-Pro.lo

Re: [Freesurfer] mri_glmfit error with aparc table flag

[Douglas N Greve]

It is a table of data, so you can't visualize it directly on anything. 
You can try using annotval2surfoverlay.m to create a surface overlay of 
the data.


On 04/19/2017 10:05 AM, miracle ozzoude wrote:
> Hello Doug,
> It worked. The issue was due to formatting error with the aparc file. 
> Also, I was trying to visualize the result on the surface using 
> freeview -f fsaverage/lh.pial -viewport 3d (clicking overlay on 
> freeview and loading the sig.mgh). However, i got an error " failed to 
> display overlay". How can I visualize the result? Thanks
> Best,
> Paul
>
> On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve 
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> You have a table of data, so no template is needed. If you put the
> --surf before the --table, it probably runs, but it will ignore
> the surface
>
>
> On 4/18/17 9:58 PM, miracoo...@gmail.com
> <mailto:miracoo...@gmail.com> wrote:
>> Thanks doug. Does it mean when using the --table flag, you can't
>> use the fsaverage template? I came across several post in the
>> forum that used "--surf fsaverage lh "‎ and it worked.
>> Best,
>> Paul
>>
>> Sent from my BlackBerry 10 smartphone.
>> *From: *Douglas Greve
>> *Sent: *Tuesday, April 18, 2017 9:52 PM
>> *To: *freesurfer@nmr.mgh.harvard.edu
>> <mailto:freesurfer@nmr.mgh.harvard.edu>
>> *Reply To: *Freesurfer support list
>> *Subject: *Re: [Freesurfer] mri_glmfit error with aparc table flag
>>
>>
>> Don't include --surf fsaverage lh. It thinks the input is a
>> surface, not a table
>>
>>
>>
>> On 4/18/17 9:21 PM, miracle ozzoude wrote:
>>> Hello freesurfer,
>>> I am trying to run mri_glmfit with the --table flag. My
>>> aparc_lh_thick_stats.txt contain entorhinal and parahippocampal
>>> thickness values for 32 subjects. I ran the glm command and
>>> received an error. Please, how can i solve this issue? I have
>>> included my command, fsgd file, contrast matrix and error below.
>>> Thanks
>>> Best,
>>> Paul
>>>
>>> GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd
>>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex
>>> --glmdir lh.thickness.glmdir
>>>
>>>
>>> ERROR= "gdfRead(): reading age.fsgd
>>>
>>> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>>>
>>> Continuous Variable Means (all subjects)
>>>
>>> 0 Age 39.9375 17.3312
>>>
>>> Class Means of each Continuous Variable
>>>
>>> 1 Group1  35.6316
>>>
>>> 2 Group2  46.2308
>>>
>>> INFO: gd2mtx_method is dods
>>>
>>> Reading source surface
>>> /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white
>>>
>>> Number of vertices 163842
>>>
>>> Number of faces327680
>>>
>>> Total area 65416.984375
>>>
>>> AvgVtxArea   0.399269
>>>
>>> AvgVtxDist   0.721953
>>>
>>> StdVtxDist   0.195470
>>>
>>>
>>> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
>>>
>>> cwd /Users/MiracleOz/Documents/improvervsdeclinermri
>>>
>>> cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd
>>> age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex
>>> --glmdir lh.thickness.glmdir
>>>
>>> sysname Darwin
>>>
>>> hostname MacBook-Pro.local
>>>
>>> machine x86_64
>>>
>>> user MiracleOz
>>>
>>> FixVertexAreaFlag = 1
>>>
>>> UseMaskWithSmoothing 1
>>>
>>> OneSampleGroupMean 0
>>>
>>> y
>>> 
>>> /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
>>>
>>> logyflag 0
>>>
>>> usedti 0
>>>
>>> FSGD age.fsgd
>>>
>>> labelmask
>>> 
>>> /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label
>>>
>>> maskinv 0
>>>
>>> glmdir lh.thickness.glmdir
>>>
>>> IllCondOK 0
>>>
>>> ReScaleX 1
&g

Re: [Freesurfer] mri_glmfit error with aparc table flag

[miracle ozzoude]

Hello Doug,
It worked. The issue was due to formatting error with the aparc file. Also,
I was trying to visualize the result on the surface using freeview -f
fsaverage/lh.pial -viewport 3d (clicking overlay on freeview and loading
the sig.mgh). However, i got an error " failed to display overlay". How can
I visualize the result? Thanks
Best,
Paul

On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> You have a table of data, so no template is needed. If you put the --surf
> before the --table, it probably runs, but it will ignore the surface
>
> On 4/18/17 9:58 PM, miracoo...@gmail.com wrote:
>
> Thanks doug. Does it mean when using the --table flag, you can't use the
> fsaverage template? I came across several post in the forum that used
> "--surf fsaverage lh "‎ and it worked.
> Best,
> Paul
>
> Sent from my BlackBerry 10 smartphone.
> *From: *Douglas Greve
> *Sent: *Tuesday, April 18, 2017 9:52 PM
> *To: *freesurfer@nmr.mgh.harvard.edu
> *Reply To: *Freesurfer support list
> *Subject: *Re: [Freesurfer] mri_glmfit error with aparc table flag
>
> Don't include --surf fsaverage lh. It thinks the input is a surface, not a
> table
>
>
>
> On 4/18/17 9:21 PM, miracle ozzoude wrote:
>
> Hello freesurfer,
> I am trying to run mri_glmfit with the --table flag. My
> aparc_lh_thick_stats.txt contain entorhinal and parahippocampal thickness
> values for 32 subjects. I ran the glm command and received an error.
> Please, how can i solve this issue? I have included my command, fsgd file,
> contrast matrix and error below. Thanks
> Best,
> Paul
>
> GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd age.fsgd
> --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir
> lh.thickness.glmdir
>
>
> ERROR= "gdfRead(): reading age.fsgd
>
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>
> Continuous Variable Means (all subjects)
>
> 0 Age 39.9375 17.3312
>
> Class Means of each Continuous Variable
>
> 1 Group1  35.6316
>
> 2 Group2  46.2308
>
> INFO: gd2mtx_method is dods
>
> Reading source surface /Users/MiracleOz/Documents/improvervsdeclinermri/
> fsaverage/surf/lh.white
>
> Number of vertices 163842
>
> Number of faces327680
>
> Total area 65416.984375
>
> AvgVtxArea   0.399269
>
> AvgVtxDist   0.721953
>
> StdVtxDist   0.195470
>
>
> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
>
> cwd /Users/MiracleOz/Documents/improvervsdeclinermri
>
> cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd age.fsgd
> --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir
> lh.thickness.glmdir
>
> sysname  Darwin
>
> hostname MacBook-Pro.local
>
> machine  x86_64
>
> user MiracleOz
>
> FixVertexAreaFlag = 1
>
> UseMaskWithSmoothing 1
>
> OneSampleGroupMean 0
>
> y/Users/MiracleOz/Documents/improvervsdeclinermri/aparc_
> lh_thick_stats.txt
>
> logyflag 0
>
> usedti  0
>
> FSGD age.fsgd
>
> labelmask  /Users/MiracleOz/Documents/improvervsdeclinermri/
> fsaverage/label/lh.cortex.label
>
> maskinv 0
>
> glmdir lh.thickness.glmdir
>
> IllCondOK 0
>
> ReScaleX 1
>
> DoFFx 0
>
> Creating output directory lh.thickness.glmdir
>
> Loading y from /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_
> lh_thick_stats.txt
>
> Found 66 data colums
>
> Found 0 data rows
>
> INFO: gd2mtx_method is dods
>
> Saving design matrix to lh.thickness.glmdir/Xg.dat
>
> Computing normalized matrix
>
> Normalized matrix condition is 32.2165
>
> Matrix condition is 20734.7
>
> Found 149955 points in label.
>
> ERROR: mri_reshape: number of elements cannot change
>
>   nv1 = 163842, nv1 = 66
>
> search space = 82219.962936
>
> ERROR: dimension mismatch between y and X.
>
>   y has 0 inputs, X has 32 rows."
>
> FSGD file: GroupDescriptorFile 1
>
> Title MOT
>
> Class Group1
>
> Class Group2
>
> Variables Age
>
> Input 01053p Group1 23
>
> Input 01054p Group1 43
>
> Input 01061p Group2 39
>
> Input 01062p Group2 19
>
> Input 01074p Group2 28
>
> .. (I have more participants)
>
>
> CONTRAST MATRIX: 1 -1 0 0
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman

Re: [Freesurfer] mri_glmfit error with aparc table flag

[miracle ozzoude]

Hello Doug,
I tried it without "--surf fsaverage lh" but i still get error. Thanks
Paul

cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C
age1.mtx --C age2.mtx --cortex --glmdir lh.thickness.glmdir

sysname  Darwin

hostname MacBook-Pro.local

machine  x86_64

user MiracoolOz

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y
/Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt

logyflag 0

usedti  0

FSGD age.fsgd

glmdir lh.thickness.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory lh.thickness.glmdir

Loading y from
/Users/MiracoolOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt

Found 66 data colums

Found 0 data rows

INFO: gd2mtx_method is dods

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

Computing normalized matrix

Normalized matrix condition is 32.2165

Matrix condition is 20734.7

search space = 66.00

ERROR: dimension mismatch between y and X.

  y has 0 inputs, X has 32 rows.








On Tue, Apr 18, 2017 at 10:03 PM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:

> You have a table of data, so no template is needed. If you put the --surf
> before the --table, it probably runs, but it will ignore the surface
>
> On 4/18/17 9:58 PM, miracoo...@gmail.com wrote:
>
> Thanks doug. Does it mean when using the --table flag, you can't use the
> fsaverage template? I came across several post in the forum that used
> "--surf fsaverage lh "‎ and it worked.
> Best,
> Paul
>
> Sent from my BlackBerry 10 smartphone.
> *From: *Douglas Greve
> *Sent: *Tuesday, April 18, 2017 9:52 PM
> *To: *freesurfer@nmr.mgh.harvard.edu
> *Reply To: *Freesurfer support list
> *Subject: *Re: [Freesurfer] mri_glmfit error with aparc table flag
>
> Don't include --surf fsaverage lh. It thinks the input is a surface, not a
> table
>
>
>
> On 4/18/17 9:21 PM, miracle ozzoude wrote:
>
> Hello freesurfer,
> I am trying to run mri_glmfit with the --table flag. My
> aparc_lh_thick_stats.txt contain entorhinal and parahippocampal thickness
> values for 32 subjects. I ran the glm command and received an error.
> Please, how can i solve this issue? I have included my command, fsgd file,
> contrast matrix and error below. Thanks
> Best,
> Paul
>
> GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd age.fsgd
> --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir
> lh.thickness.glmdir
>
>
> ERROR= "gdfRead(): reading age.fsgd
>
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
>
> Continuous Variable Means (all subjects)
>
> 0 Age 39.9375 17.3312
>
> Class Means of each Continuous Variable
>
> 1 Group1  35.6316
>
> 2 Group2  46.2308
>
> INFO: gd2mtx_method is dods
>
> Reading source surface /Users/MiracleOz/Documents/improvervsdeclinermri/
> fsaverage/surf/lh.white
>
> Number of vertices 163842
>
> Number of faces327680
>
> Total area 65416.984375
>
> AvgVtxArea   0.399269
>
> AvgVtxDist   0.721953
>
> StdVtxDist   0.195470
>
>
> $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
>
> cwd /Users/MiracleOz/Documents/improvervsdeclinermri
>
> cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd age.fsgd
> --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir
> lh.thickness.glmdir
>
> sysname  Darwin
>
> hostname MacBook-Pro.local
>
> machine  x86_64
>
> user MiracleOz
>
> FixVertexAreaFlag = 1
>
> UseMaskWithSmoothing 1
>
> OneSampleGroupMean 0
>
> y/Users/MiracleOz/Documents/improvervsdeclinermri/aparc_
> lh_thick_stats.txt
>
> logyflag 0
>
> usedti  0
>
> FSGD age.fsgd
>
> labelmask  /Users/MiracleOz/Documents/improvervsdeclinermri/
> fsaverage/label/lh.cortex.label
>
> maskinv 0
>
> glmdir lh.thickness.glmdir
>
> IllCondOK 0
>
> ReScaleX 1
>
> DoFFx 0
>
> Creating output directory lh.thickness.glmdir
>
> Loading y from /Users/MiracleOz/Documents/improvervsdeclinermri/aparc_
> lh_thick_stats.txt
>
> Found 66 data colums
>
> Found 0 data rows
>
> INFO: gd2mtx_method is dods
>
> Saving design matrix to lh.thickness.glmdir/Xg.dat
>
> Computing normalized matrix
>
> Normalized matrix condition is 32.2165
>
> Matrix condition is 20734.7
>
> Found 149955 points in label.
>
> ERROR: mri_reshape: number of elements cannot change
>
>   nv1 = 163842, nv1 = 66
>
> search space = 82219.962936
>
> ERROR: dimension mismatch between y and X.
>
>   y has 0 inputs, X has 32 rows."
>
> FSGD file: GroupDescriptorFile 1
>
> Title MOT
>
> Class Group1
>

Re: [Freesurfer] mri_glmfit error with aparc table flag

[Douglas Greve]

You have a table of data, so no template is needed. If you put the 
--surf before the --table, it probably runs, but it will ignore the surface



On 4/18/17 9:58 PM, miracoo...@gmail.com wrote:
Thanks doug. Does it mean when using the --table flag, you can't use 
the fsaverage template? I came across several post in the forum that 
used "--surf fsaverage lh "‎ and it worked.

Best,
Paul

Sent from my BlackBerry 10 smartphone.
*From: *Douglas Greve
*Sent: *Tuesday, April 18, 2017 9:52 PM
*To: *freesurfer@nmr.mgh.harvard.edu
*Reply To: *Freesurfer support list
*Subject: *Re: [Freesurfer] mri_glmfit error with aparc table flag


Don't include --surf fsaverage lh. It thinks the input is a surface, 
not a table




On 4/18/17 9:21 PM, miracle ozzoude wrote:

Hello freesurfer,
I am trying to run mri_glmfit with the --table flag. My 
aparc_lh_thick_stats.txt contain entorhinal and parahippocampal 
thickness values for 32 subjects. I ran the glm command and received 
an error. Please, how can i solve this issue? I have included my 
command, fsgd file, contrast matrix and error below. Thanks

Best,
Paul

GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd 
age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex 
--glmdir lh.thickness.glmdir



ERROR= "gdfRead(): reading age.fsgd

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

Continuous Variable Means (all subjects)

0 Age 39.9375 17.3312

Class Means of each Continuous Variable

1 Group1 35.6316

2 Group2 46.2308

INFO: gd2mtx_method is dods

Reading source surface 
/Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white


Number of vertices 163842

Number of faces327680

Total area 65416.984375

AvgVtxArea   0.399269

AvgVtxDist   0.721953

StdVtxDist   0.195470


$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $

cwd /Users/MiracleOz/Documents/improvervsdeclinermri

cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd 
age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex 
--glmdir lh.thickness.glmdir


sysname  Darwin

hostname MacBook-Pro.local

machine  x86_64

user MiracleOz

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y 
/Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt


logyflag 0

usedti  0

FSGD age.fsgd

labelmask 
/Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label


maskinv 0

glmdir lh.thickness.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory lh.thickness.glmdir

Loading y from 
/Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt


Found 66 data colums

Found 0 data rows

INFO: gd2mtx_method is dods

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

Computing normalized matrix

Normalized matrix condition is 32.2165

Matrix condition is 20734.7

Found 149955 points in label.

ERROR: mri_reshape: number of elements cannot change

  nv1 = 163842, nv1 = 66

search space = 82219.962936

ERROR: dimension mismatch between y and X.

  y has 0 inputs, X has 32 rows."

FSGD file: GroupDescriptorFile 1

Title MOT

Class Group1

Class Group2

Variables Age

Input 01053p Group1 23

Input 01054p Group1 43

Input 01061p Group2 39

Input 01062p Group2 19

Input 01074p Group2 28

.. (I have more participants)


CONTRAST MATRIX: 1 -1 0 0



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Re: [Freesurfer] mri_glmfit error with aparc table flag

[miracooloz]

  Thanks doug. Does it mean when using the --table flag, you can't use the fsaverage template? I came across several post in the forum that used "--surf fsaverage lh "‎ and it worked. Best, Paul Sent from my BlackBerry 10 smartphone.From: Douglas GreveSent: Tuesday, April 18, 2017 9:52 PMTo: freesurfer@nmr.mgh.harvard.eduReply To: Freesurfer support listSubject: Re: [Freesurfer] mri_glmfit error with aparc table flag
  

  
  
Don't include --surf fsaverage lh. It thinks the input is a
  surface, not a table



On 4/18/17 9:21 PM, miracle ozzoude
  wrote:


  Hello freesurfer, 
I am trying to run mri_glmfit with the --table flag. My
  aparc_lh_thick_stats.txt contain entorhinal and
  parahippocampal thickness values for 32 subjects. I ran the
  glm command and received an error. Please, how can i solve
  this issue? I have included my command, fsgd file, contrast
  matrix and error below. Thanks 
Best, 
Paul


GLM command: mri_glmfit
--table aparc_lh_thick_stats.txt --fsgd age.fsgd --C
age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir
lh.thickness.glmdir

  


ERROR= "gdfRead(): reading age.fsgd


  INFO: DeMeanFlag
  keyword not found, DeMeaning will NOT be done.
  Continuous Variable
  Means (all subjects)
  0 Age 39.9375
  17.3312
  Class Means of each
  Continuous Variable
  1 Group1  35.6316 
  2 Group2  46.2308 
  INFO: gd2mtx_method
  is dods
  Reading source
  surface
  /Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white
  Number of vertices
  163842
  Number of faces   
  327680
  Total area        
  65416.984375
  AvgVtxArea      
  0.399269
  AvgVtxDist      
  0.721953
  StdVtxDist      
  0.195470
  
  
  $Id: mri_glmfit.c,v
  1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $
  cwd
  /Users/MiracleOz/Documents/improvervsdeclinermri
  cmdline
  mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd
  age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh
  --cortex --glmdir lh.thickness.glmdir 
  sysname  Darwin
  hostname
  MacBook-Pro.local
  machine  x86_64
  user     MiracleOz
  FixVertexAreaFlag =
  1
  UseMaskWithSmoothing
      1
  OneSampleGroupMean
  0
  y   
/Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
  logyflag 0
  usedti  0
  FSGD age.fsgd
  labelmask 
/Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label
  maskinv 0
  glmdir
  lh.thickness.glmdir
  IllCondOK 0
  ReScaleX 1
  DoFFx 0
  Creating output
  directory lh.thickness.glmdir
  Loading y from
/Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt
  Found 66 data
  colums
  Found 0 data rows
  INFO: gd2mtx_method
  is dods
  Saving design
  matrix to lh.thickness.glmdir/Xg.dat
  Computing
  normalized matrix
  Normalized matrix
  condition is 32.2165
  Matrix condition is
  20734.7
  Found 149955 points
  in label.
  ERROR: mri_reshape:
  number of elements cannot change
    nv1 = 163842, nv1
  = 66
  search space =
  82219.962936
  ERROR: dimension
  mismatch between y and X.
    y has 0 inputs, X
  has 32 rows." 
  FSGD file: GroupDescriptorFile
  1
  Title MOT
  Class Group1
  Class Group2
  Variables Age
  Input 01053p Group1
  23
  Input 01054p Group1
  43
  

Re: [Freesurfer] mri_glmfit error with aparc table flag

[Douglas Greve]

Don't include --surf fsaverage lh. It thinks the input is a surface, not 
a table




On 4/18/17 9:21 PM, miracle ozzoude wrote:

Hello freesurfer,
I am trying to run mri_glmfit with the --table flag. My 
aparc_lh_thick_stats.txt contain entorhinal and parahippocampal 
thickness values for 32 subjects. I ran the glm command and received 
an error. Please, how can i solve this issue? I have included my 
command, fsgd file, contrast matrix and error below. Thanks

Best,
Paul

GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd 
age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex 
--glmdir lh.thickness.glmdir



ERROR= "gdfRead(): reading age.fsgd

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

Continuous Variable Means (all subjects)

0 Age 39.9375 17.3312

Class Means of each Continuous Variable

1 Group1  35.6316

2 Group2  46.2308

INFO: gd2mtx_method is dods

Reading source surface 
/Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white


Number of vertices 163842

Number of faces 327680

Total area 65416.984375

AvgVtxArea 0.399269

AvgVtxDist 0.721953

StdVtxDist 0.195470


$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $

cwd /Users/MiracleOz/Documents/improvervsdeclinermri

cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd 
age.fsgd --C age1.mtx --C age2.mtx --surf fsaverage lh --cortex 
--glmdir lh.thickness.glmdir


sysname  Darwin

hostname MacBook-Pro.local

machine  x86_64

user MiracleOz

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y 
/Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt


logyflag 0

usedti  0

FSGD age.fsgd

labelmask 
/Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label


maskinv 0

glmdir lh.thickness.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory lh.thickness.glmdir

Loading y from 
/Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt


Found 66 data colums

Found 0 data rows

INFO: gd2mtx_method is dods

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

Computing normalized matrix

Normalized matrix condition is 32.2165

Matrix condition is 20734.7

Found 149955 points in label.

ERROR: mri_reshape: number of elements cannot change

  nv1 = 163842, nv1 = 66

search space = 82219.962936

ERROR: dimension mismatch between y and X.

  y has 0 inputs, X has 32 rows."

FSGD file: GroupDescriptorFile 1

Title MOT

Class Group1

Class Group2

Variables Age

Input 01053p Group1 23

Input 01054p Group1 43

Input 01061p Group2 39

Input 01062p Group2 19

Input 01074p Group2 28

.. (I have more participants)


CONTRAST MATRIX: 1 -1 0 0



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[Freesurfer] mri_glmfit error with aparc table flag

[miracle ozzoude]

Hello freesurfer,
I am trying to run mri_glmfit with the --table flag. My
aparc_lh_thick_stats.txt contain entorhinal and parahippocampal thickness
values for 32 subjects. I ran the glm command and received an error.
Please, how can i solve this issue? I have included my command, fsgd file,
contrast matrix and error below. Thanks
Best,
Paul

GLM command: mri_glmfit --table aparc_lh_thick_stats.txt --fsgd age.fsgd
--C age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir
lh.thickness.glmdir


ERROR= "gdfRead(): reading age.fsgd

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

Continuous Variable Means (all subjects)

0 Age 39.9375 17.3312

Class Means of each Continuous Variable

1 Group1  35.6316

2 Group2  46.2308

INFO: gd2mtx_method is dods

Reading source surface
/Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/surf/lh.white

Number of vertices 163842

Number of faces327680

Total area 65416.984375

AvgVtxArea   0.399269

AvgVtxDist   0.721953

StdVtxDist   0.195470


$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $

cwd /Users/MiracleOz/Documents/improvervsdeclinermri

cmdline mri_glmfit.bin --table aparc_lh_thick_stats.txt --fsgd age.fsgd --C
age1.mtx --C age2.mtx --surf fsaverage lh --cortex --glmdir
lh.thickness.glmdir

sysname  Darwin

hostname MacBook-Pro.local

machine  x86_64

user MiracleOz

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y
/Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt

logyflag 0

usedti  0

FSGD age.fsgd

labelmask
/Users/MiracleOz/Documents/improvervsdeclinermri/fsaverage/label/lh.cortex.label

maskinv 0

glmdir lh.thickness.glmdir

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory lh.thickness.glmdir

Loading y from
/Users/MiracleOz/Documents/improvervsdeclinermri/aparc_lh_thick_stats.txt

Found 66 data colums

Found 0 data rows

INFO: gd2mtx_method is dods

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

Computing normalized matrix

Normalized matrix condition is 32.2165

Matrix condition is 20734.7

Found 149955 points in label.

ERROR: mri_reshape: number of elements cannot change

  nv1 = 163842, nv1 = 66

search space = 82219.962936

ERROR: dimension mismatch between y and X.

  y has 0 inputs, X has 32 rows."

FSGD file: GroupDescriptorFile 1

Title MOT

Class Group1

Class Group2

Variables Age

Input 01053p Group1 23

Input 01054p Group1 43

Input 01061p Group2 39

Input 01062p Group2 19

Input 01074p Group2 28

.. (I have more participants)


CONTRAST MATRIX: 1 -1 0 0
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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] mri_glmfit error

[Douglas N Greve]

I can't tell from the glmfit command line what you are trying to do. 
Generally, the GLM is run on group data and you specify an average brain 
(eg, fsaverage) as the --surf.

On 07/14/2016 06:10 AM, Chatzi, Vasiliki wrote:
>
>
> Dear Developers,
>
>
> I am trying to run the mri_glmfit command and I get two 
> different errors for two different subjects. Please find 
> details below. I would be really grateful if you could provide any advice.
>
>
>
> Error1
>
> setenv SUBJECTS_DIR ./
>
> mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt 
> --no-contrasts-ok --surf subject1 lh
>
> gdfReadHeader: reading fsgd_test2.txt
>
> INFO: gd2mtx_method is dods
>
> Reading source surface .//subject1/surf/lh.white
>
> Number of vertices 167703
>
> Number of faces335402
>
> Total area 108706.031250
>
> AvgVtxArea   0.648206
>
> AvgVtxDist   0.881642
>
> StdVtxDist   0.250483
>
> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
>
> cwd /home/test
>
> cmdline mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt 
> --no-contrasts-ok --surf subject1 lh
>
> sysname  Linux
>
> hostname
>
> machine  x86_64
>
> user
>
> FixVertexAreaFlag = 1
>
> UseMaskWithSmoothing 1
>
> OneSampleGroupMean 0
>
> y/home/test/lh.10.lgi.mgh
>
> logyflag 0
>
> usedti  0
>
> FSGD fsgd_test2.txt
>
> labelmask  .//subject1ii/label/lh.cortex.label
>
> maskinv 0
>
> glmdir ./
>
> IllCondOK 0
>
> ReScaleX 1
>
> DoFFx 0
>
> Creating output directory ./
>
> Loading y from /home/test/lh.10.lgi.mgh
>
> INFO: gd2mtx_method is dods
>
> Saving design matrix to .//Xg.dat
>
> Normalized matrix condition is 1
>
> Matrix condition is 1
>
> Found 158404 points in label.
>
> ERROR: mri_reshape: number of elements cannot change
>
>   nv1 = 167703, nv1 = 163842
>
> Pruning voxels by thr: 0.00
>
> Found 163842 voxels in mask
>
> Saving mask to .//mask.mgh
>
> Reshaping mriglm->mask...
>
> ERROR: mri_reshape: number of elements cannot change
>
>   nv1 = 163842, nv1 = 167703
>
> search space = 108705.102552
>
> DOF = 0
>
> ERROR: DOF = 0
>
>
>
> Error 2
> setenv SUBJECTS_DIR ./
> mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt 
> --no-contrasts-ok --surf subject2 lh
> gdfReadHeader: reading fsgd_test2.txt
> INFO: gd2mtx_method is dods
> Reading source surface .//subject2/surf/lh.white
> Number of vertices 129318
> Number of faces258632
> Total area 86174.742188
> AvgVtxArea   0.666379
> AvgVtxDist   0.893985
> StdVtxDist   0.260921
> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
> cwd /home/test
> cmdline mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt 
> --no-contrasts-ok --surf subject2 lh
> sysname  Linux
> hostname
> machine  x86_64
> user
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 0
> y/home/test/lh.10.lgi.mgh
> logyflag 0
> usedti  0
> FSGD fsgd_test2.txt
> labelmask  .//subject2/label/lh.cortex.label
> maskinv 0
> glmdir ./
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
> Creating output directory ./
> Loading y from /home/test/lh.10.lgi.mgh
> INFO: gd2mtx_method is dods
> Saving design matrix to .//Xg.dat
> Normalized matrix condition is 1
> Matrix condition is 1
> Found 121215 points in label.
> ERROR: mri_reshape: number of elements cannot change
>   nv1 = 129318, nv1 = 163842
> Pruning voxels by thr: 0.00
> Segmentation fault
>
> Bets wishes,
> Vasiliki
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

[Douglas N Greve]

It does not look like the variables are demeaned (your FSGD file below)

Variables Age eTIV EnglishParityRT
Input Math_5001m Monolingual_male 18 1865790.30866 -8952.208
Input Math_5002m Monolingual_female 19 1520429.68796 -4605.208
Input Math_5003m Monolingual_male 19 1749716.72939 -39407.208333
Input Math_5004m Monolingual_female 18 1589109.27022 -17967.208333
Input Math_5005m Monolingual_male 21 1472295.15211 19531.791667
Input Math_5006m Monolingual_male 18 1580381.40566 -17027.208333
Input Math_5007m Monolingual_male 20 1813373.55024 16152.791667
Input Math_5008m Monolingual_male 21 1638616.48007 -9074.208
Input Math_5009m Monolingual_female 21 1297920.49281 61860.791667
Input Math_5010m Monolingual_female 18 1634762.57845 -22671.208333
Input Math_5011m Monolingual_female 21 1602611.42141 12763.791667
Input Math_5014m Monolingual_male 21 1632452.66476 9395.2916669


On 07/18/2016 01:31 PM, Jennifer Legault wrote:
> Hi Doug,
>
> Thank you for your response.  The current fsgd file I sent you was 
> with the covariates demeaned x 100, as I saw you recommend that to 
> someone else.  We previously tried doing just the demeaned values 
> without multiplying by 100, and that still had the badly scaled 
> error.  Do you think we should take the demeaned x 100 covariates and 
> divide them by the standard deviation?  Or would it be better to take 
> regular demeaned values and divide them by the standard deviation?
>
> Best,
>
> Jennifer Legault
>
> On Mon, Jul 18, 2016 at 12:43 PM, Douglas N Greve 
> > wrote:
>
> This is almost surely a problem with scaling as your covariates are
> huge. Try subtracting the mean and dividing by the stddev before
> entering into the FSGD file. Compute the means and stddevs across all
> subjects.
> doug
>
> On 07/11/2016 03:20 PM, Jennifer Legault wrote:
> > Hi Freesurfer Experts,
> >
> > I am trying to run mri_glmfit and while 90% of my files work,
> some of
> > them display the error below.  I have tried demeaning, and then
> tried
> > multiplying this value by 100, and I still get the same error.  Any
> > feedback would be greatly appreciated.
> >
> > mris_preproc done
> > srcsubject = fsaverage
> > srcval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00.mgh
> > srctype=
> > trgsubject = fsaverage
> > trgval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> > trgtype=
> > srcsurfreg = sphere.reg
> > trgsurfreg = sphere.reg
> > srchemi= rh
> > trghemi= rh
> > frame  = 0
> > fwhm-in= 0
> > fwhm-out   = 0
> > label-src  = (null)
> > label-trg  = (null)
> > OKToRevFaceOrder  = 1
> > Reading source surface reg
> >
> /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.sphere.reg
> > Loading source data
> > INFO: trgsubject = srcsubject
> > Saving target data
> > Saving to rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> > gdfReadHeader: reading
> >
> 
> /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
> > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> > Continuous Variable Means (all subjects)
> > 0 Age 19.5833 1.32025
> > 1 eTIV 1.61645e+06 145343
> > 2 EnglishParityRT 0.00012207 25139.1
> > Class Means of each Continuous Variable
> > 1 Monolingual_male  19.7143 1678946.5893 -4197.2796
> > 2 Monolingual_female  19.4000 1528966.6750 5876.1917
> > INFO: gd2mtx_method is dods
> > Reading source surface
> > /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.white
> > Number of vertices 163842
> > Number of faces327680
> > Total area 65020.765625
> > AvgVtxArea   0.396850
> > AvgVtxDist   0.717994
> > StdVtxDist   0.193566
> >
> > $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
> > cwd /gpfs/scratch/jtl190/Math_reconstruction
> > cmdline mri_glmfit --y
> > rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh --fsgd
> >
> 
> /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
> > --C
> >
> 
> /gpfs/scratch/jtl190/Contrast_files/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt
> > --surf fsaverage rh --cortex --glmdir
> > rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
> > sysname  Linux
> > hostname cyberstar129.hpc.rcc.psu.edu
> 
> > 
> > machine  x86_64
> > user jtl190
> > FixVertexAreaFlag = 1
> > UseMaskWithSmoothing 1
> > OneSampleGroupMean 0
> > y
> >
> 
> /gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh

Re: [Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

[Jennifer Legault]

Hi Doug,

Thank you for your response.  The current fsgd file I sent you was with the
covariates demeaned x 100, as I saw you recommend that to someone else.  We
previously tried doing just the demeaned values without multiplying by 100,
and that still had the badly scaled error.  Do you think we should take the
demeaned x 100 covariates and divide them by the standard deviation?  Or
would it be better to take regular demeaned values and divide them by the
standard deviation?

Best,

Jennifer Legault

On Mon, Jul 18, 2016 at 12:43 PM, Douglas N Greve  wrote:

> This is almost surely a problem with scaling as your covariates are
> huge. Try subtracting the mean and dividing by the stddev before
> entering into the FSGD file. Compute the means and stddevs across all
> subjects.
> doug
>
> On 07/11/2016 03:20 PM, Jennifer Legault wrote:
> > Hi Freesurfer Experts,
> >
> > I am trying to run mri_glmfit and while 90% of my files work, some of
> > them display the error below.  I have tried demeaning, and then tried
> > multiplying this value by 100, and I still get the same error.  Any
> > feedback would be greatly appreciated.
> >
> > mris_preproc done
> > srcsubject = fsaverage
> > srcval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00.mgh
> > srctype=
> > trgsubject = fsaverage
> > trgval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> > trgtype=
> > srcsurfreg = sphere.reg
> > trgsurfreg = sphere.reg
> > srchemi= rh
> > trghemi= rh
> > frame  = 0
> > fwhm-in= 0
> > fwhm-out   = 0
> > label-src  = (null)
> > label-trg  = (null)
> > OKToRevFaceOrder  = 1
> > Reading source surface reg
> > /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.sphere.reg
> > Loading source data
> > INFO: trgsubject = srcsubject
> > Saving target data
> > Saving to rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> > gdfReadHeader: reading
> >
> /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
> > INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> > Continuous Variable Means (all subjects)
> > 0 Age 19.5833 1.32025
> > 1 eTIV 1.61645e+06 145343
> > 2 EnglishParityRT 0.00012207 25139.1
> > Class Means of each Continuous Variable
> > 1 Monolingual_male  19.7143 1678946.5893 -4197.2796
> > 2 Monolingual_female  19.4000 1528966.6750 5876.1917
> > INFO: gd2mtx_method is dods
> > Reading source surface
> > /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.white
> > Number of vertices 163842
> > Number of faces327680
> > Total area 65020.765625
> > AvgVtxArea   0.396850
> > AvgVtxDist   0.717994
> > StdVtxDist   0.193566
> >
> > $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
> > cwd /gpfs/scratch/jtl190/Math_reconstruction
> > cmdline mri_glmfit --y
> > rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh --fsgd
> >
> /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
> > --C
> >
> /gpfs/scratch/jtl190/Contrast_files/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt
> > --surf fsaverage rh --cortex --glmdir
> > rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
> > sysname  Linux
> > hostname cyberstar129.hpc.rcc.psu.edu
> > 
> > machine  x86_64
> > user jtl190
> > FixVertexAreaFlag = 1
> > UseMaskWithSmoothing 1
> > OneSampleGroupMean 0
> > y
> >
> /gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> > logyflag 0
> > usedti  0
> > FSGD
> >
> /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
> > labelmask
> >  /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/label/rh.cortex.label
> > maskinv 0
> > glmdir rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
> > IllCondOK 0
> > ReScaleX 1
> > DoFFx 0
> > Creating output directory
> > rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
> > Loading y from
> >
> /gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> > INFO: gd2mtx_method is dods
> > Saving design matrix to
> > rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir/Xg.dat
> > Normalized matrix condition is 22568.9
> > Design matrix --
> >  1.000   0.000   18.000   0.000   1865790.250   0.000  -8952.208   0.000;
> >  0.000   1.000   0.000   19.000   0.000   1520429.625 0.000  -4605.208;
> >  1.000   0.000   19.000   0.000   1749716.750   0.000  -39407.207
>  0.000;
> >  0.000   1.000   0.000   18.000   0.000   1589109.250 0.000  -17967.209;
> >  1.000   0.000   21.000   0.000   1472295.125   0.000 19531.791   0.000;
> >  1.000   0.000   18.000   0.000   1580381.375   0.000  -17027.209
>  0.000;
> >  1.000   0.000   20.000   0.000   1813373.500   0.000 16152.792   0.000;
> >  1.000   0.000   21.000   0.000   1638616.500   0.000  -9074.208   0.000;
> >  0.000   1.000   0.000   21.000   0.000   1297920.500 0.000   61860.793;

Re: [Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

[Douglas N Greve]

This is almost surely a problem with scaling as your covariates are 
huge. Try subtracting the mean and dividing by the stddev before 
entering into the FSGD file. Compute the means and stddevs across all 
subjects.
doug

On 07/11/2016 03:20 PM, Jennifer Legault wrote:
> Hi Freesurfer Experts,
>
> I am trying to run mri_glmfit and while 90% of my files work, some of 
> them display the error below.  I have tried demeaning, and then tried 
> multiplying this value by 100, and I still get the same error.  Any 
> feedback would be greatly appreciated.
>
> mris_preproc done
> srcsubject = fsaverage
> srcval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00.mgh
> srctype=
> trgsubject = fsaverage
> trgval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> trgtype=
> srcsurfreg = sphere.reg
> trgsurfreg = sphere.reg
> srchemi= rh
> trghemi= rh
> frame  = 0
> fwhm-in= 0
> fwhm-out   = 0
> label-src  = (null)
> label-trg  = (null)
> OKToRevFaceOrder  = 1
> Reading source surface reg 
> /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.sphere.reg
> Loading source data
> INFO: trgsubject = srcsubject
> Saving target data
> Saving to rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> gdfReadHeader: reading 
> /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
> INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
> Continuous Variable Means (all subjects)
> 0 Age 19.5833 1.32025
> 1 eTIV 1.61645e+06 145343
> 2 EnglishParityRT 0.00012207 25139.1
> Class Means of each Continuous Variable
> 1 Monolingual_male  19.7143 1678946.5893 -4197.2796
> 2 Monolingual_female  19.4000 1528966.6750 5876.1917
> INFO: gd2mtx_method is dods
> Reading source surface 
> /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.white
> Number of vertices 163842
> Number of faces327680
> Total area 65020.765625
> AvgVtxArea   0.396850
> AvgVtxDist   0.717994
> StdVtxDist   0.193566
>
> $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
> cwd /gpfs/scratch/jtl190/Math_reconstruction
> cmdline mri_glmfit --y 
> rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh --fsgd 
> /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
>  
> --C 
> /gpfs/scratch/jtl190/Contrast_files/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt
>  
> --surf fsaverage rh --cortex --glmdir 
> rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
> sysname  Linux
> hostname cyberstar129.hpc.rcc.psu.edu 
> 
> machine  x86_64
> user jtl190
> FixVertexAreaFlag = 1
> UseMaskWithSmoothing 1
> OneSampleGroupMean 0
> y 
>  
> /gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> logyflag 0
> usedti  0
> FSGD 
> /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
> labelmask 
>  /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/label/rh.cortex.label
> maskinv 0
> glmdir rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
> IllCondOK 0
> ReScaleX 1
> DoFFx 0
> Creating output directory 
> rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
> Loading y from 
> /gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
> INFO: gd2mtx_method is dods
> Saving design matrix to 
> rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir/Xg.dat
> Normalized matrix condition is 22568.9
> Design matrix --
>  1.000   0.000   18.000   0.000   1865790.250   0.000  -8952.208   0.000;
>  0.000   1.000   0.000   19.000   0.000   1520429.625 0.000  -4605.208;
>  1.000   0.000   19.000   0.000   1749716.750   0.000  -39407.207   0.000;
>  0.000   1.000   0.000   18.000   0.000   1589109.250 0.000  -17967.209;
>  1.000   0.000   21.000   0.000   1472295.125   0.000 19531.791   0.000;
>  1.000   0.000   18.000   0.000   1580381.375   0.000  -17027.209   0.000;
>  1.000   0.000   20.000   0.000   1813373.500   0.000 16152.792   0.000;
>  1.000   0.000   21.000   0.000   1638616.500   0.000  -9074.208   0.000;
>  0.000   1.000   0.000   21.000   0.000   1297920.500 0.000   61860.793;
>  0.000   1.000   0.000   18.000   0.000   1634762.625 0.000  -22671.209;
>  0.000   1.000   0.000   21.000   0.000   1602611.375 0.000   12763.792;
>  1.000   0.000   21.000   0.000   1632452.625   0.000 9395.292   0.000;
> 
> ERROR: matrix is ill-conditioned or badly scaled, condno = 22568.9
> 
> Possible problem with experimental design:
> Check for duplicate entries and/or lack of range of
> continuous variables within a class.
> If you seek help with this problem, make sure to send:
>   1. Your command line:
> mri_glmfit --y 
> rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh --fsgd 
> /gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
>  
> --C 
> 

[Freesurfer] mri_glmfit error

[Chatzi, Vasiliki]

Dear Developers,


I am trying to run the mri_glmfit command and I get two different errors for 
two different subjects. Please find details below. I would be really grateful 
if you could provide any advice.



Error1

setenv SUBJECTS_DIR ./

mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt 
--no-contrasts-ok --surf subject1 lh

gdfReadHeader: reading fsgd_test2.txt

INFO: gd2mtx_method is dods

Reading source surface .//subject1/surf/lh.white

Number of vertices 167703

Number of faces335402

Total area 108706.031250

AvgVtxArea   0.648206

AvgVtxDist   0.881642

StdVtxDist   0.250483

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $

cwd /home/test

cmdline mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt 
--no-contrasts-ok --surf subject1 lh

sysname  Linux

hostname

machine  x86_64

user

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

OneSampleGroupMean 0

y/home/test/lh.10.lgi.mgh

logyflag 0

usedti  0

FSGD fsgd_test2.txt

labelmask  .//subject1ii/label/lh.cortex.label

maskinv 0

glmdir ./

IllCondOK 0

ReScaleX 1

DoFFx 0

Creating output directory ./

Loading y from /home/test/lh.10.lgi.mgh

INFO: gd2mtx_method is dods

Saving design matrix to .//Xg.dat

Normalized matrix condition is 1

Matrix condition is 1

Found 158404 points in label.

ERROR: mri_reshape: number of elements cannot change

  nv1 = 167703, nv1 = 163842

Pruning voxels by thr: 0.00

Found 163842 voxels in mask

Saving mask to .//mask.mgh

Reshaping mriglm->mask...

ERROR: mri_reshape: number of elements cannot change

  nv1 = 163842, nv1 = 167703

search space = 108705.102552

DOF = 0

ERROR: DOF = 0


Error 2
setenv SUBJECTS_DIR ./
mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt 
--no-contrasts-ok --surf subject2 lh
gdfReadHeader: reading fsgd_test2.txt
INFO: gd2mtx_method is dods
Reading source surface .//subject2/surf/lh.white
Number of vertices 129318
Number of faces258632
Total area 86174.742188
AvgVtxArea   0.666379
AvgVtxDist   0.893985
StdVtxDist   0.260921
$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /home/test
cmdline mri_glmfit --glmdir ./ --y lh.10.lgi.mgh --fsgd fsgd_test2.txt 
--no-contrasts-ok --surf subject2 lh
sysname  Linux
hostname
machine  x86_64
user
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y/home/test/lh.10.lgi.mgh
logyflag 0
usedti  0
FSGD fsgd_test2.txt
labelmask  .//subject2/label/lh.cortex.label
maskinv 0
glmdir ./
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory ./
Loading y from /home/test/lh.10.lgi.mgh
INFO: gd2mtx_method is dods
Saving design matrix to .//Xg.dat
Normalized matrix condition is 1
Matrix condition is 1
Found 121215 points in label.
ERROR: mri_reshape: number of elements cannot change
  nv1 = 129318, nv1 = 163842
Pruning voxels by thr: 0.00
Segmentation fault

Bets wishes,
Vasiliki


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[Freesurfer] mri_glmfit error: Matrix is ill-conditioned or badly scaled

[Jennifer Legault]

Hi Freesurfer Experts,

I am trying to run mri_glmfit and while 90% of my files work, some of them
display the error below.  I have tried demeaning, and then tried
multiplying this value by 100, and I still get the same error.  Any
feedback would be greatly appreciated.

mris_preproc done
srcsubject = fsaverage
srcval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00.mgh
srctype=
trgsubject = fsaverage
trgval = rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
trgtype=
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= rh
trghemi= rh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = (null)
label-trg  = (null)
OKToRevFaceOrder  = 1
Reading source surface reg
/gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.sphere.reg
Loading source data
INFO: trgsubject = srcsubject
Saving target data
Saving to rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
gdfReadHeader: reading
/gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 19.5833 1.32025
1 eTIV 1.61645e+06 145343
2 EnglishParityRT 0.00012207 25139.1
Class Means of each Continuous Variable
1 Monolingual_male  19.7143 1678946.5893 -4197.2796
2 Monolingual_female  19.4000 1528966.6750 5876.1917
INFO: gd2mtx_method is dods
Reading source surface
/gpfs/scratch/jtl190/Math_reconstruction/fsaverage/surf/rh.white
Number of vertices 163842
Number of faces327680
Total area 65020.765625
AvgVtxArea   0.396850
AvgVtxDist   0.717994
StdVtxDist   0.193566

$Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $
cwd /gpfs/scratch/jtl190/Math_reconstruction
cmdline mri_glmfit --y
rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh --fsgd
/gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
--C
/gpfs/scratch/jtl190/Contrast_files/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt
--surf fsaverage rh --cortex --glmdir
rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
sysname  Linux
hostname cyberstar129.hpc.rcc.psu.edu
machine  x86_64
user jtl190
FixVertexAreaFlag = 1
UseMaskWithSmoothing 1
OneSampleGroupMean 0
y
 
/gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
logyflag 0
usedti  0
FSGD
/gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
labelmask
 /gpfs/scratch/jtl190/Math_reconstruction/fsaverage/label/rh.cortex.label
maskinv 0
glmdir rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
IllCondOK 0
ReScaleX 1
DoFFx 0
Creating output directory rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
Loading y from
/gpfs/scratch/jtl190/Math_reconstruction/rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
INFO: gd2mtx_method is dods
Saving design matrix to
rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir/Xg.dat
Normalized matrix condition is 22568.9
Design matrix --
 1.000   0.000   18.000   0.000   1865790.250   0.000  -8952.208   0.000;
 0.000   1.000   0.000   19.000   0.000   1520429.625   0.000  -4605.208;
 1.000   0.000   19.000   0.000   1749716.750   0.000  -39407.207   0.000;
 0.000   1.000   0.000   18.000   0.000   1589109.250   0.000  -17967.209;
 1.000   0.000   21.000   0.000   1472295.125   0.000   19531.791   0.000;
 1.000   0.000   18.000   0.000   1580381.375   0.000  -17027.209   0.000;
 1.000   0.000   20.000   0.000   1813373.500   0.000   16152.792   0.000;
 1.000   0.000   21.000   0.000   1638616.500   0.000  -9074.208   0.000;
 0.000   1.000   0.000   21.000   0.000   1297920.500   0.000   61860.793;
 0.000   1.000   0.000   18.000   0.000   1634762.625   0.000  -22671.209;
 0.000   1.000   0.000   21.000   0.000   1602611.375   0.000   12763.792;
 1.000   0.000   21.000   0.000   1632452.625   0.000   9395.292   0.000;

ERROR: matrix is ill-conditioned or badly scaled, condno = 22568.9

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit --y rh.mono_EnglishParityRT_age_gender_TIV.volume.00B.mgh
--fsgd
/gpfs/scratch/jtl190/FSGD_files/fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
--C
/gpfs/scratch/jtl190/Contrast_files/Contrast_math_monly_EnglishParityRT_a_g_TIV.txt
--surf fsaverage rh --cortex --glmdir
rh.mono_EnglishParityRT_age_gender_TIV_100.glmdir
  2. The FSGD file (if using one)
  3. And the design matrix above


I am also attaching the FSGD file.

Best,

Jennifer Legault


fsgd_math_mono_EnglishParityRT_age_gender_TIV_demean100.fsgd
Description: Binary data
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[Freesurfer] mri_glmfit error FSGD file exceeds the maximum allowed 2000

[Avram Holmes]

FreeSurfer List,

I am attempting to run an analyses on 2051 participants. However, when I reach 
the mri_glmfit stage I receive the following error. 

ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the maximum allowed 
2000

Is there a work around for this? 

Thank you in advance for any help you can offer,
Avram

Avram Holmes PhD
Assistant Professor
Department of Psychology, Yale University
Email: avram.hol...@yale.edu
Office: 203-436-9240
Web: holmeslab.commons.yale.edu

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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] mri_glmfit error FSGD file exceeds the maximum allowed 2000

[Douglas N Greve]

This is hard coded unfortunately. I've bumped it up to 20k in the most 
recent version. I've put a linux version here

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit



On 03/16/2015 06:38 AM, Avram Holmes wrote:
 FreeSurfer List,

 I am attempting to run an analyses on 2051 participants. However, when 
 I reach the mri_glmfit stage I receive the following error.

 ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the 
 maximum allowed 2000

 Is there a work around for this?

 Thank you in advance for any help you can offer,
 Avram

 Avram Holmes PhD
 Assistant Professor
 Department of Psychology, Yale University
 Email: avram.hol...@yale.edu mailto:avram.hol...@yale.edu
 Office: 203-436-9240
 Web: holmeslab.commons.yale.edu http://holmeslab.commons.yale.edu



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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

[lindsay hanford]

Hi Doug!

Thank you very much for your reply. I made the fsgd file in a plain-text
file using the textedit program on a Mac and when that didn't work I tried
modifying in the terminal window using: nano -w g4v1.73.fsgd.
This also didn't solve the problem. I am not sure what to try next.

Lindsay

On Thu, Dec 11, 2014 at 9:09 AM, lindsay hanford lindsay.hanf...@gmail.com
wrote:

 Hello,

 Has anyone had a chance to look at this? I still haven't been able to
 solve the problem.
 Thanks!

 Lindsay

 On Mon, Dec 1, 2014 at 2:41 PM, lindsay hanford lindsay.hanf...@gmail.com
  wrote:

 Hello Freesurfer Experts!

 I am encountering the dreaded mri_glmfit error:  matrix is
 ill-conditioned or badly scaled, condno = 1e+08. I have tried to
 troubleshoot how to solve this problem from other inquiries, however, I
 still have had no luck. I am trying to run a 4 group 1 variable analysis:
 with diagnosis being my variable of interest and trying to regress out the
 effects of sex and age.

   1. Command line:
 mri_glmfit --y lh.10.73.SZHC.mgh --fsgd g4v1.73.fsgd dods --C
 SZ-HC.intercept.73.mtx --surf fsaverage lh --cortex --glmdir g4v1.73.lh
   2. The FSGD file (if using one) (see attached)
   3. And the design matrix:
0.5 0.5 -0.5 -0.5 0 0 0 0 (or see attached)

 To the best of my knowledge, all my files are the right format and I
 believe I have adequate number of participants per group?
 I also tried mean centering my age variable. I had success when I ran
 just a two group analysis (diagnosis) not controlling for sex or age,
 however, as soon as I try to run four groups, I encounter this error. I
 have no idea how to proceed.

 I am looking forward to your response!
 Thanks,


 Lindsay

 --
 Lindsay Hanford, BSc, PhD Candidate
 McMaster Integrative Neuroscience Discovery  Study | *Department of
 Psychology, Neuroscience  Behaviour *
 McMaster University *|* 1280 Main Street West, PC329 Psychology Building
 *|* Hamilton, ON, L8S 4L8
 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com




-- 
Lindsay Hanford, BSc, PhD Candidate
McMaster Integrative Neuroscience Discovery  Study | *Department of
Psychology, Neuroscience  Behaviour *
McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|*
 Hamilton, ON, L8S 4L8
905 525 9140 x24784 *|* lindsay.hanf...@gmail.com
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Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

[Douglas N Greve]

The file I looked at had a bunch of carriage returns (try looking at it 
with more or less or cat). As long as those are in there, it will create 
an error.

Try running this and using the new one
cat g4v1.73.fsgd | sed 's/\r/\n/g'  new.g4v1.73.fsgd

On 12/12/2014 12:09 PM, lindsay hanford wrote:
 Hi Doug!

 Thank you very much for your reply. I made the fsgd file in a 
 plain-text file using the textedit program on a Mac and when that 
 didn't work I tried modifying in the terminal window using: nano -w 
 g4v1.73.fsgd.
 This also didn't solve the problem. I am not sure what to try next.

 Lindsay

 On Thu, Dec 11, 2014 at 9:09 AM, lindsay hanford 
 lindsay.hanf...@gmail.com mailto:lindsay.hanf...@gmail.com wrote:

 Hello,

 Has anyone had a chance to look at this? I still haven't been able
 to solve the problem.
 Thanks!

 Lindsay

 On Mon, Dec 1, 2014 at 2:41 PM, lindsay hanford
 lindsay.hanf...@gmail.com mailto:lindsay.hanf...@gmail.com wrote:

 Hello Freesurfer Experts!

 I am encountering the dreaded mri_glmfit error:  matrix is
 ill-conditioned or badly scaled, condno = 1e+08. I have tried
 to troubleshoot how to solve this problem from other
 inquiries, however, I still have had no luck. I am trying to
 run a 4 group 1 variable analysis: with diagnosis being my
 variable of interest and trying to regress out the effects of
 sex and age.

   1. Command line:
 mri_glmfit --y lh.10.73.SZHC.mgh --fsgd g4v1.73.fsgd dods
 --C SZ-HC.intercept.73.mtx --surf fsaverage lh --cortex
 --glmdir g4v1.73.lh
   2. The FSGD file (if using one) (see attached)
   3. And the design matrix:
0.5 0.5 -0.5 -0.5 0 0 0 0 (or see attached)

 To the best of my knowledge, all my files are the right format
 and I believe I have adequate number of participants per group?
 I also tried mean centering my age variable. I had success
 when I ran just a two group analysis (diagnosis) not
 controlling for sex or age, however, as soon as I try to run
 four groups, I encounter this error. I have no idea how to
 proceed.

 I am looking forward to your response!
 Thanks,


 Lindsay

 -- 
 Lindsay Hanford, BSc, PhD Candidate
 McMaster Integrative Neuroscience Discovery  Study|
 *Department of Psychology, Neuroscience  Behaviour *
 McMaster University *|* 1280 Main Street West, PC329
 Psychology Building *|* Hamilton, ON, L8S 4L8
 905 525 9140 x24784
 tel:905%20525%209140%20x24784***|*lindsay.hanf...@gmail.com
 mailto:lindsay.hanf...@gmail.com




 -- 
 Lindsay Hanford, BSc, PhD Candidate
 McMaster Integrative Neuroscience Discovery  Study| *Department of 
 Psychology, Neuroscience  Behaviour *
 McMaster University *|* 1280 Main Street West, PC329 Psychology 
 Building *|* Hamilton, ON, L8S 4L8
 905 525 9140 x24784***|*lindsay.hanf...@gmail.com 
 mailto:lindsay.hanf...@gmail.com


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

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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dispose of the e-mail.

Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

[lindsay hanford]

Thank you Doug! I replaced all my spaces with new spaces and it worked!
Much appreciated!

Lindsay

On Fri, Dec 12, 2014 at 12:09 PM, lindsay hanford lindsay.hanf...@gmail.com
 wrote:

 Hi Doug!

 Thank you very much for your reply. I made the fsgd file in a plain-text
 file using the textedit program on a Mac and when that didn't work I tried
 modifying in the terminal window using: nano -w g4v1.73.fsgd.
 This also didn't solve the problem. I am not sure what to try next.

 Lindsay

 On Thu, Dec 11, 2014 at 9:09 AM, lindsay hanford 
 lindsay.hanf...@gmail.com wrote:

 Hello,

 Has anyone had a chance to look at this? I still haven't been able to
 solve the problem.
 Thanks!

 Lindsay

 On Mon, Dec 1, 2014 at 2:41 PM, lindsay hanford 
 lindsay.hanf...@gmail.com wrote:

 Hello Freesurfer Experts!

 I am encountering the dreaded mri_glmfit error:  matrix is
 ill-conditioned or badly scaled, condno = 1e+08. I have tried to
 troubleshoot how to solve this problem from other inquiries, however, I
 still have had no luck. I am trying to run a 4 group 1 variable analysis:
 with diagnosis being my variable of interest and trying to regress out the
 effects of sex and age.

   1. Command line:
 mri_glmfit --y lh.10.73.SZHC.mgh --fsgd g4v1.73.fsgd dods --C
 SZ-HC.intercept.73.mtx --surf fsaverage lh --cortex --glmdir g4v1.73.lh
   2. The FSGD file (if using one) (see attached)
   3. And the design matrix:
0.5 0.5 -0.5 -0.5 0 0 0 0 (or see attached)

 To the best of my knowledge, all my files are the right format and I
 believe I have adequate number of participants per group?
 I also tried mean centering my age variable. I had success when I ran
 just a two group analysis (diagnosis) not controlling for sex or age,
 however, as soon as I try to run four groups, I encounter this error. I
 have no idea how to proceed.

 I am looking forward to your response!
 Thanks,


 Lindsay

 --
 Lindsay Hanford, BSc, PhD Candidate
 McMaster Integrative Neuroscience Discovery  Study | *Department of
 Psychology, Neuroscience  Behaviour *
 McMaster University *|* 1280 Main Street West, PC329 Psychology
 Building *|* Hamilton, ON, L8S 4L8
 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com




 --
 Lindsay Hanford, BSc, PhD Candidate
 McMaster Integrative Neuroscience Discovery  Study | *Department of
 Psychology, Neuroscience  Behaviour *
 McMaster University *|* 1280 Main Street West, PC329 Psychology Building
 *|* Hamilton, ON, L8S 4L8
 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com



-- 
Lindsay Hanford, BSc, PhD Candidate
McMaster Integrative Neuroscience Discovery  Study | *Department of
Psychology, Neuroscience  Behaviour *
McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|*
 Hamilton, ON, L8S 4L8
905 525 9140 x24784 *|* lindsay.hanf...@gmail.com
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

[lindsay hanford]

Hello,

Has anyone had a chance to look at this? I still haven't been able to solve
the problem.
Thanks!

Lindsay

On Mon, Dec 1, 2014 at 2:41 PM, lindsay hanford lindsay.hanf...@gmail.com
wrote:

 Hello Freesurfer Experts!

 I am encountering the dreaded mri_glmfit error:  matrix is ill-conditioned
 or badly scaled, condno = 1e+08. I have tried to troubleshoot how to solve
 this problem from other inquiries, however, I still have had no luck. I am
 trying to run a 4 group 1 variable analysis: with diagnosis being my
 variable of interest and trying to regress out the effects of sex and age.

   1. Command line:
 mri_glmfit --y lh.10.73.SZHC.mgh --fsgd g4v1.73.fsgd dods --C
 SZ-HC.intercept.73.mtx --surf fsaverage lh --cortex --glmdir g4v1.73.lh
   2. The FSGD file (if using one) (see attached)
   3. And the design matrix:
0.5 0.5 -0.5 -0.5 0 0 0 0 (or see attached)

 To the best of my knowledge, all my files are the right format and I
 believe I have adequate number of participants per group?
 I also tried mean centering my age variable. I had success when I ran just
 a two group analysis (diagnosis) not controlling for sex or age, however,
 as soon as I try to run four groups, I encounter this error. I have no idea
 how to proceed.

 I am looking forward to your response!
 Thanks,


 Lindsay

 --
 Lindsay Hanford, BSc, PhD Candidate
 McMaster Integrative Neuroscience Discovery  Study | *Department of
 Psychology, Neuroscience  Behaviour *
 McMaster University *|* 1280 Main Street West, PC329 Psychology Building
 *|* Hamilton, ON, L8S 4L8
 905 525 9140 x24784 *|* lindsay.hanf...@gmail.com

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

[Douglas N Greve]

Your FSGD file appears to have been made under windows or using an 
editor that is not simple text. The contrast matrix looks ok.

doug

On 12/01/2014 02:41 PM, lindsay hanford wrote:
 Hello Freesurfer Experts!

 I am encountering the dreaded mri_glmfit error:  matrix is 
 ill-conditioned or badly scaled, condno = 1e+08. I have tried to 
 troubleshoot how to solve this problem from other inquiries, however, 
 I still have had no luck. I am trying to run a 4 group 1 variable 
 analysis: with diagnosis being my variable of interest and trying to 
 regress out the effects of sex and age.

   1. Command line:
 mri_glmfit --y lh.10.73.SZHC.mgh --fsgd g4v1.73.fsgd dods --C 
 SZ-HC.intercept.73.mtx --surf fsaverage lh --cortex --glmdir g4v1.73.lh
   2. The FSGD file (if using one) (see attached)
   3. And the design matrix:
0.5 0.5 -0.5 -0.5 0 0 0 0 (or see attached)

 To the best of my knowledge, all my files are the right format and I 
 believe I have adequate number of participants per group?
 I also tried mean centering my age variable. I had success when I ran 
 just a two group analysis (diagnosis) not controlling for sex or age, 
 however, as soon as I try to run four groups, I encounter this error. 
 I have no idea how to proceed.

 I am looking forward to your response!
 Thanks,


 Lindsay

 -- 
 Lindsay Hanford, BSc, PhD Candidate
 McMaster Integrative Neuroscience Discovery  Study| *Department of 
 Psychology, Neuroscience  Behaviour *
 McMaster University *|* 1280 Main Street West, PC329 Psychology 
 Building *|* Hamilton, ON, L8S 4L8
 905 525 9140 x24784***|*lindsay.hanf...@gmail.com 
 mailto:lindsay.hanf...@gmail.com


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

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_glmfit error

[Douglas Greve]

You have a --C that is not followed by a contrast file.
doug

On 11/26/14 10:58 PM, Bronwyn Overs wrote:

Dear Freesurfer Mailing list,

I have been attempting to run the following command in freesurfer v5.3.0:

mri_glmfit --y site-gender-group-prothaplotype.thick.lh.10.mgh --fsgd 
site-gender-group-prothaplotype.fsgd dods --C me_site-BrisVsMelb.mtx 
--C me_site-BrisVsPer.mtx --C me_site-MelbVsPer.mtx --C --surf 
fsaverage lh --cortex --glmdir 
site-gender-group-prothaplotype.thick.lh.glmdir


Unfortunely, I keep getting the following error:
ERROR: Option lh unknown

Do you know why this would be?

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au http://neura.edu.au

Follow @neuraustralia on twitter 
https://twitter.com/neuraustraliaFollow NeuRA on facebook 
https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to 
the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe




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Re: [Freesurfer] mri_glmfit error

[Bronwyn Overs]

Thanks Douglas.

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au http://neura.edu.au

Follow @neuraustralia on twitter 
https://twitter.com/neuraustraliaFollow NeuRA on facebook 
https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the 
NeuRA Magazine http://www.neura.edu.au/help-research/subscribe


On 3/12/2014 3:53 pm, Douglas Greve wrote:


You have a --C that is not followed by a contrast file.
doug

On 11/26/14 10:58 PM, Bronwyn Overs wrote:

Dear Freesurfer Mailing list,

I have been attempting to run the following command in freesurfer 
v5.3.0:


mri_glmfit --y site-gender-group-prothaplotype.thick.lh.10.mgh --fsgd 
site-gender-group-prothaplotype.fsgd dods --C me_site-BrisVsMelb.mtx 
--C me_site-BrisVsPer.mtx --C me_site-MelbVsPer.mtx --C --surf 
fsaverage lh --cortex --glmdir 
site-gender-group-prothaplotype.thick.lh.glmdir


Unfortunely, I keep getting the following error:
ERROR: Option lh unknown

Do you know why this would be?

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au http://neura.edu.au

Follow @neuraustralia on twitter 
https://twitter.com/neuraustraliaFollow NeuRA on facebook 
https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to 
the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe




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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] mri_glmfit error: matrix is ill-conditioned or badly scaled, condno = 1e+08

[lindsay hanford]

Hello Freesurfer Experts!

I am encountering the dreaded mri_glmfit error:  matrix is ill-conditioned
or badly scaled, condno = 1e+08. I have tried to troubleshoot how to solve
this problem from other inquiries, however, I still have had no luck. I am
trying to run a 4 group 1 variable analysis: with diagnosis being my
variable of interest and trying to regress out the effects of sex and age.

  1. Command line:
mri_glmfit --y lh.10.73.SZHC.mgh --fsgd g4v1.73.fsgd dods --C
SZ-HC.intercept.73.mtx --surf fsaverage lh --cortex --glmdir g4v1.73.lh
  2. The FSGD file (if using one) (see attached)
  3. And the design matrix:
   0.5 0.5 -0.5 -0.5 0 0 0 0 (or see attached)

To the best of my knowledge, all my files are the right format and I
believe I have adequate number of participants per group?
I also tried mean centering my age variable. I had success when I ran just
a two group analysis (diagnosis) not controlling for sex or age, however,
as soon as I try to run four groups, I encounter this error. I have no idea
how to proceed.

I am looking forward to your response!
Thanks,


Lindsay

-- 
Lindsay Hanford, BSc, PhD Candidate
McMaster Integrative Neuroscience Discovery  Study | *Department of
Psychology, Neuroscience  Behaviour *
McMaster University *|* 1280 Main Street West, PC329 Psychology Building *|*
 Hamilton, ON, L8S 4L8
905 525 9140 x24784 *|* lindsay.hanf...@gmail.com


g4v1.73.fsgd
Description: Binary data


SZ-HC.intercept.73.mtx
Description: Binary data
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dispose of the e-mail.

[Freesurfer] mri_glmfit error

[Bronwyn Overs]

Dear Freesurfer Mailing list,

I have been attempting to run the following command in freesurfer v5.3.0:

mri_glmfit --y site-gender-group-prothaplotype.thick.lh.10.mgh --fsgd 
site-gender-group-prothaplotype.fsgd dods --C me_site-BrisVsMelb.mtx --C 
me_site-BrisVsPer.mtx --C me_site-MelbVsPer.mtx --C --surf fsaverage lh 
--cortex --glmdir site-gender-group-prothaplotype.thick.lh.glmdir


Unfortunely, I keep getting the following error:
ERROR: Option lh unknown

Do you know why this would be?

Kind regards,

Bronwyn Overs
Research Assistant

Neuroscience Research Australia

Neuroscience Research Australia
Margarete Ainsworth Building
Barker Street Randwick Sydney NSW 2031 Australia
*M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265

neura.edu.au http://neura.edu.au

Follow @neuraustralia on twitter 
https://twitter.com/neuraustraliaFollow NeuRA on facebook 
https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the 
NeuRA Magazine http://www.neura.edu.au/help-research/subscribe


___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_glmfit error

[Douglas N Greve]

On 12/18/2013 11:14 PM, Rujing Zha wrote:
 Hi Doug and others,
 Thanks Doug.
 For the 2nd problem: I understand orthogonalization between nuisance 
 variables. I just want to test the difference between two group mean 
 pial thickness controling the age and edu (if it is necessary to 
 control the age and sex). So I guess I have two option: one: I can 
 select one of them discarding the other one in the fsgd. the other 
 one: I select both of them, and ignoring the high correlation.
 For the 3rd problem: As I just want to know the difference between 2 
 group pial thickness controling some other factors which may explain 
 my result, so I guess I just donot consider the sex as a nuisance factor.
 Is that appropriate?
I don't know. It is not a question for me to answer since it depends on 
the data.
 There is a new problem for me:
 I also want to do a partial analysis between pial thickness analysis 
 and behavior score. The numbers of class in fsgd file are the same as 
 this one except adding another colume for the score. Is this correct?
Yes

 Thanks.
 All the best.
 2013-12-19
 
 /Rujing Zha/
 
 *发件人：*Douglas Greve gr...@nmr.mgh.harvard.edu
 *发送时间：*2013-12-19 11:34
 *主题：*Re: [Freesurfer] mri_glmfit error
 *收件人：*Rujing Zhacharujing...@163.com
 *抄送：*freesurferfreesurfer@nmr.mgh.harvard.edu

 On 12/18/13 10:26 PM, Rujing Zha wrote:
 Hi Doug and others,
 Thanks Doug.
 I modifiled my number of class in the fsgd which can be got in the 
 attachment.
 And I am confused with 3 problems:
 1st: Is what I modified proper?
 Yes
 2nd: How can I deal with my high correlation between age and edu?
 If they are nuisance variables, then you could orthogonalize one with 
 respect to the other. If you really want to test for a difference in 
 groups for the age slope or the edu slope, then there is nothing you 
 can do except get more subjects.
 3rd: Is it necessary to tell mri_glmfit to distinguish which subject 
 is female or male in each class if dividing all subjects into 2 
 classes (i.e con and IA )?
 If you only have con and IA, you cannot have a gender factor. If you 
 think that a gender factor is really necessary, then you need to get 
 more females.
 doug

 Thanks in advance.
 All the best.
 2013-12-19
 
 /Rujing Zha/
 
 *发件人：*Douglas N Greve gr...@nmr.mgh.harvard.edu
 *发送时间：*2013-12-19 04:59
 *主题：*Re: [Freesurfer] mri_glmfit error
 *收件人：*freesurferfreesurfer@nmr.mgh.harvard.edu
 *抄送：*
 Could be several things. You only have two IA_female and and only 3
 con_female. Also, the age and edu are highly correlated. I would try
 creating a single IA group with males and females and a single con group
 doug
 On 12/18/2013 11:21 AM, Rujing Zha wrote:
  Hi all,
  I try to run mri_glmfit, but it export
  ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
  
  Possible problem with experimental design:
  Check for duplicate entries and/or lack of range of
  continuous variables within a class..
  I upload the data in the attachment, and the glmfit_output is the
  standard output of the mri_glmfit.
  Thanks.
  All the best.
  2013-12-19
   

  /Rujing Zha/
 
 
  ___
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  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 -- 
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 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422
 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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 e-mail 

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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Re: [Freesurfer] mri_glmfit error

[Rujing Zha]

Hi Doug and others,
Thanks Doug.
All the best.

2013-12-20



Rujing Zha



发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu
发送时间：2013-12-20 00:11
主题：Re: [Freesurfer] mri_glmfit error
收件人：Rujing Zhacharujing...@163.com
抄送：freesurferfreesurfer@nmr.mgh.harvard.edu


On 12/18/2013 11:14 PM, Rujing Zha wrote: 
 Hi Doug and others, 
 Thanks Doug. 
 For the 2nd problem: I understand orthogonalization between nuisance  
 variables. I just want to test the difference between two group mean  
 pial thickness controling the age and edu (if it is necessary to  
 control the age and sex). So I guess I have two option: one: I can  
 select one of them discarding the other one in the fsgd. the other  
 one: I select both of them, and ignoring the high correlation. 
 For the 3rd problem: As I just want to know the difference between 2  
 group pial thickness controling some other factors which may explain  
 my result, so I guess I just donot consider the sex as a nuisance factor. 
 Is that appropriate? 
I don't know. It is not a question for me to answer since it depends on  
the data. 
 There is a new problem for me: 
 I also want to do a partial analysis between pial thickness analysis  
 and behavior score. The numbers of class in fsgd file are the same as  
 this one except adding another colume for the score. Is this correct? 
Yes 

 Thanks. 
 All the best. 
 2013-12-19 
  
 /Rujing Zha/ 
  
 *发件人：*Douglas Greve gr...@nmr.mgh.harvard.edu 
 *发送时间：*2013-12-19 11:34 
 *主题：*Re: [Freesurfer] mri_glmfit error 
 *收件人：*Rujing Zhacharujing...@163.com 
 *抄送：*freesurferfreesurfer@nmr.mgh.harvard.edu 
 
 On 12/18/13 10:26 PM, Rujing Zha wrote: 
 Hi Doug and others, 
 Thanks Doug. 
 I modifiled my number of class in the fsgd which can be got in the  
 attachment. 
 And I am confused with 3 problems: 
 1st: Is what I modified proper? 
 Yes 
 2nd: How can I deal with my high correlation between age and edu? 
 If they are nuisance variables, then you could orthogonalize one with  
 respect to the other. If you really want to test for a difference in  
 groups for the age slope or the edu slope, then there is nothing you  
 can do except get more subjects. 
 3rd: Is it necessary to tell mri_glmfit to distinguish which subject  
 is female or male in each class if dividing all subjects into 2  
 classes (i.e con and IA )? 
 If you only have con and IA, you cannot have a gender factor. If you  
 think that a gender factor is really necessary, then you need to get  
 more females. 
 doug 
 
 Thanks in advance. 
 All the best. 
 2013-12-19 
  
 /Rujing Zha/ 
  
 *发件人：*Douglas N Greve gr...@nmr.mgh.harvard.edu 
 *发送时间：*2013-12-19 04:59 
 *主题：*Re: [Freesurfer] mri_glmfit error 
 *收件人：*freesurferfreesurfer@nmr.mgh.harvard.edu 
 *抄送：* 
 Could be several things. You only have two IA_female and and only 3 
 con_female. Also, the age and edu are highly correlated. I would try 
 creating a single IA group with males and females and a single con group 
 doug 
 On 12/18/2013 11:21 AM, Rujing Zha wrote: 
  Hi all, 
  I try to run mri_glmfit, but it export 
  ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 
   
  Possible problem with experimental design: 
  Check for duplicate entries and/or lack of range of 
  continuous variables within a class.. 
  I upload the data in the attachment, and the glmfit_output is the 
  standard output of the mri_glmfit. 
  Thanks. 
  All the best. 
  2013-12-19 
    
 
  /Rujing Zha/ 
  
  
  ___ 
  Freesurfer mailing list 
  Freesurfer@nmr.mgh.harvard.edu 
  https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
 --  
 Douglas N. Greve, Ph.D. 
 MGH-NMR Center 
 gr...@nmr.mgh.harvard.edu 
 Phone Number: 617-724-2358 
 Fax: 617-726-7422 
 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
 The information in this e-mail is intended only for the person to whom it is 
  
 
 addressed. If you believe this e-mail was sent to you in error and the 
 e-mail  
 
 contains patient information, please contact the Partners Compliance 
 HelpLine at  
 
 http://www.partners.org/complianceline . If the e-mail was sent to you in 
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 but does not contain patient information, please contact the sender and 
 properly

[Freesurfer] mri_glmfit error

[Rujing Zha]

Hi all,
I try to run mri_glmfit, but it export 
ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class..
I upload the data in the attachment, and the glmfit_output is the standard 
output of the mri_glmfit.
Thanks.
All the best.

2013-12-19



Rujing Zha

age_edu.fsgd
Description: Binary data


glmfit_output
Description: Binary data


lh-Diff-con-IA-Intercept-thickness.mtx
Description: Binary data


mri_glmfit.log
Description: Binary data
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] mri_glmfit error

[Douglas N Greve]

Could be several things. You only have two IA_female and and only 3 
con_female. Also, the age and edu are highly correlated. I would try 
creating a single IA group with males and females and a single con group
doug


On 12/18/2013 11:21 AM, Rujing Zha wrote:
 Hi all,
 I try to run mri_glmfit, but it export
 ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
 
 Possible problem with experimental design:
 Check for duplicate entries and/or lack of range of
 continuous variables within a class..
 I upload the data in the attachment, and the glmfit_output is the 
 standard output of the mri_glmfit.
 Thanks.
 All the best.
 2013-12-19
 
 /Rujing Zha/


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

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_glmfit error

[Rujing Zha]

Hi Doug and others,
Thanks Doug.
I modifiled my number of class in the fsgd which can be got in the attachment.
And I am confused with 3 problems:
1st: Is what I modified proper?
2nd: How can I deal with my high correlation between age and edu?
3rd: Is it necessary to tell mri_glmfit to distinguish which subject is female 
or male in each class if dividing all subjects into 2 classes (i.e con and IA 
)? 
Thanks in advance.
All the best.

2013-12-19



Rujing Zha



发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu
发送时间：2013-12-19 04:59
主题：Re: [Freesurfer] mri_glmfit error
收件人：freesurferfreesurfer@nmr.mgh.harvard.edu
抄送：


Could be several things. You only have two IA_female and and only 3  
con_female. Also, the age and edu are highly correlated. I would try  
creating a single IA group with males and females and a single con group 
doug 


On 12/18/2013 11:21 AM, Rujing Zha wrote: 
 Hi all, 
 I try to run mri_glmfit, but it export 
 ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 
  
 Possible problem with experimental design: 
 Check for duplicate entries and/or lack of range of 
 continuous variables within a class.. 
 I upload the data in the attachment, and the glmfit_output is the  
 standard output of the mri_glmfit. 
 Thanks. 
 All the best. 
 2013-12-19 
  
 /Rujing Zha/ 
 
 
 ___ 
 Freesurfer mailing list 
 Freesurfer@nmr.mgh.harvard.edu 
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 

--  
Douglas N. Greve, Ph.D. 
MGH-NMR Center 
gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358 
Fax: 617-726-7422 

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 
www.nmr.mgh.harvard.edu/facility/filedrop/index.html 
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 

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but does not contain patient information, please contact the sender and 
properly 
dispose of the e-mail. 

age_edu.fsgd
Description: Binary data
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Re: [Freesurfer] mri_glmfit error

[Douglas Greve]

On 12/18/13 10:26 PM, Rujing Zha wrote:

Hi Doug and others,
Thanks Doug.
I modifiled my number of class in the fsgd which can be got in the 
attachment.

And I am confused with 3 problems:
1st: Is what I modified proper?

Yes

2nd: How can I deal with my high correlation between age and edu?
If they are nuisance variables, then you could orthogonalize one with 
respect to the other. If you really want to test for a difference in 
groups for the age slope or the edu slope, then there is nothing you can 
do except get more subjects.
3rd: Is it necessary to tell mri_glmfit to distinguish which subject 
is female or male in each class if dividing all subjects into 2 
classes (i.e con and IA )?
If you only have con and IA, you cannot have a gender factor. If you 
think that a gender factor is really necessary, then you need to get 
more females.

doug


Thanks in advance.
All the best.
2013-12-19

/Rujing Zha/

*发件人：*Douglas N Greve gr...@nmr.mgh.harvard.edu
*发送时间：*2013-12-19 04:59
*主题：*Re: [Freesurfer] mri_glmfit error
*收件人：*freesurferfreesurfer@nmr.mgh.harvard.edu
*抄送：*
Could be several things. You only have two IA_female and and only 3
con_female. Also, the age and edu are highly correlated. I would try
creating a single IA group with males and females and a single con group
doug
On 12/18/2013 11:21 AM, Rujing Zha wrote:
 Hi all,
 I try to run mri_glmfit, but it export
 ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
 
 Possible problem with experimental design:
 Check for duplicate entries and/or lack of range of
 continuous variables within a class..
 I upload the data in the attachment, and the glmfit_output is the
 standard output of the mri_glmfit.
 Thanks.
 All the best.
 2013-12-19
  


 /Rujing Zha/


 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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but does not contain patient information, please contact the sender and properly 


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Re: [Freesurfer] mri_glmfit error

[Rujing Zha]

Hi Doug and others,
Thanks Doug.
For the 2nd problem: I understand orthogonalization between nuisance variables. 
I just want to test the difference between two group mean pial thickness 
controling the age and edu (if it is necessary to control the age and sex). So 
I guess I have two option: one: I can select one of them discarding the other 
one in the fsgd. the other one: I select both of them, and ignoring the high 
correlation.
For the 3rd problem: As I just want to know the difference between 2 group pial 
thickness controling some other factors which may explain my result, so I guess 
I just donot consider the sex as a nuisance factor.
Is that appropriate?
There is a new problem for me:
I also want to do a partial analysis between pial thickness analysis and 
behavior score. The numbers of class in fsgd file are the same as this one 
except adding another colume for the score. Is this correct?
Thanks.
All the best.

2013-12-19



Rujing Zha



发件人：Douglas Greve gr...@nmr.mgh.harvard.edu
发送时间：2013-12-19 11:34
主题：Re: [Freesurfer] mri_glmfit error
收件人：Rujing Zhacharujing...@163.com
抄送：freesurferfreesurfer@nmr.mgh.harvard.edu



On 12/18/13 10:26 PM, Rujing Zha wrote:

Hi Doug and others,
Thanks Doug.
I modifiled my number of class in the fsgd which can be got in the attachment.
And I am confused with 3 problems:
1st: Is what I modified proper?
Yes

2nd: How can I deal with my high correlation between age and edu?
If they are nuisance variables, then you could orthogonalize one with respect 
to the other. If you really want to test for a difference in groups for the age 
slope or the edu slope, then there is nothing you can do except get more 
subjects.

3rd: Is it necessary to tell mri_glmfit to distinguish which subject is female 
or male in each class if dividing all subjects into 2 classes (i.e con and IA 
)? 
If you only have con and IA, you cannot have a gender factor. If you think that 
a gender factor is really necessary, then you need to get more females.
doug


Thanks in advance.
All the best.

2013-12-19



Rujing Zha



发件人：Douglas N Greve gr...@nmr.mgh.harvard.edu
发送时间：2013-12-19 04:59
主题：Re: [Freesurfer] mri_glmfit error
收件人：freesurferfreesurfer@nmr.mgh.harvard.edu
抄送：


Could be several things. You only have two IA_female and and only 3  
con_female. Also, the age and edu are highly correlated. I would try  
creating a single IA group with males and females and a single con group 
doug 


On 12/18/2013 11:21 AM, Rujing Zha wrote: 
 Hi all, 
 I try to run mri_glmfit, but it export 
 ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 
  
 Possible problem with experimental design: 
 Check for duplicate entries and/or lack of range of 
 continuous variables within a class.. 
 I upload the data in the attachment, and the glmfit_output is the  
 standard output of the mri_glmfit. 
 Thanks. 
 All the best. 
 2013-12-19 
  
 /Rujing Zha/ 
 
 
 ___ 
 Freesurfer mailing list 
 Freesurfer@nmr.mgh.harvard.edu 
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 

--  
Douglas N. Greve, Ph.D. 
MGH-NMR Center 
gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358 
Fax: 617-726-7422 

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 
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[Freesurfer] mri_glmfit error: negative DOF -10

[Robert Schulz]

Hello,

I am using mri_glmfit to perform a correlation analysis between some 
surface-based DTI measures and a behavioural outcome (grip), aiming to 
correct for scannertyp (C,I,W), handedness (R,L) as discrete variables and 
age (AGE) and duration (Mo) as continuous covariates. Please find the fsgd 
file, the contrast file and the calculated Xg down below.
However, I get the follow error:

DOF = -10
ERROR: DOF = -10 (the complete output is attached)

I would be grateful if somebody could help. I already tried it with demeaned 
data, z-transformed data, it doesn't help.

Thank you for your help,

Robert




fsgd file:
GroupDescriptorFile 1
Title OSGM
Class CR
Class CL
Class WL
Class WR
Class IR
Class IL
Variables Age Mo Grip
Input c02 CR 52 85 0.250
Input c04 CR 71 27 0.652
Input c05 CL 63 12 0.788
Input c06 WL 77 26 0.438
Input c07 WR 61 13 0.717
Input c10 IR 68 9 0.730
Input c11 IL 63 13 0.934
Input c12 IL 29 12 1.170
Input c13 IR 46 12 0.964
Input c14 IR 75 14 0.655
Input c15 IL 68 13 1.098
Input c16 IR 69 12 1.028
Input c18 WL 40 20 0.698
Input c19 WL 53 13 0.547

contrast file:
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1

design matrix:

+1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +52.0 +0.0 
+0.0 +0.0 +0.0 +0.0 +85.0 +0.0 +0.0 +0.0 
+0.0 +0.0 +0.25000 +0.0 +0.0 +0.0 +0.0 +0.0
+1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +71.0 +0.0 
+0.0 +0.0 +0.0 +0.0 +27.0 +0.0 +0.0 +0.0 
+0.0 +0.0 +0.65200 +0.0 +0.0 +0.0 +0.0 +0.0
+0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +63.0 
+0.0 +0.0 +0.0 +0.0 +0.0 +12.0 +0.0 +0.0 
+0.0 +0.0 +0.0 +0.78800 +0.0 +0.0 +0.0 +0.0
+0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 
+77.0 +0.0 +0.0 +0.0 +0.0 +0.0 +26.0 +0.0 
+0.0 +0.0 +0.0 +0.0 +0.43800 +0.0 +0.0 +0.0
+0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 
+0.0 +61.0 +0.0 +0.0 +0.0 +0.0 +0.0 +13.0 
+0.0 +0.0 +0.0 +0.0 +0.0 +0.71700 +0.0 +0.0
+0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 
+0.0 +0.0 +68.0 +0.0 +0.0 +0.0 +0.0 +0.0 
+9.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.73000 +0.0
+0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 
+0.0 +0.0 +0.0 +63.0 +0.0 +0.0 +0.0 +0.0 
+0.0 +13.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.93400
+0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 
+0.0 +0.0 +0.0 +29.0 +0.0 +0.0 +0.0 +0.0 
+0.0 +12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.17000
+0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 
+0.0 +0.0 +46.0 +0.0 +0.0 +0.0 +0.0 +0.0 
+12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.96400 +0.0
+0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 
+0.0 +0.0 +75.0 +0.0 +0.0 +0.0 +0.0 +0.0 
+14.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.65500 +0.0
+0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 
+0.0 +0.0 +0.0 +68.0 +0.0 +0.0 +0.0 +0.0 
+0.0 +13.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.09800
+0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 
+0.0 +0.0 +69.0 +0.0 +0.0 +0.0 +0.0 +0.0 
+12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.02800 +0.0
+0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 
+40.0 +0.0 +0.0 +0.0 +0.0 +0.0 +20.0 +0.0 
+0.0 +0.0 +0.0 +0.0 +0.69800 +0.0 +0.0 +0.0
+0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 
+53.0 +0.0 +0.0 +0.0 +0.0 +0.0 +13.0 +0.0 
+0.0 +0.0 +0.0 +0.0 +0.54700 +0.0 +0.0 +0.0

output:

gdfReadHeader: reading 
/home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/glmout/corr.fsgd
INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
Continuous Variable Means (all subjects)
0 Age 59.6429 13.4462
1 Mo 20.0714 18.7444
2 Grip 0.762071 0.248599
Class Means of each Continuous Variable
1 CR 61.5000 56. 0.4510
2 CL 63. 12. 0.7880
3 WL 56.6667 19.6667 0.5610
4 WR 61. 13. 0.7170
5 IR 64.5000 11.7500 0.8442
6 IL 53. 12.6667 1.0673
INFO: gd2mtx_method is dods
Reading source surface 
/home/schulz/freesurfer/subjects/premotorstroke/fsaverage/surf/lh.white
Number of vertices 163842
Number of faces 327680
Total area 65416.648438
AvgVtxArea 0.399267

Re: [Freesurfer] mri_glmfit error: negative DOF -10

[Douglas Greve]

It usually means that the number of subjects in the input is less (10 
less) than the number of regressors. It looks like you have about 14 
input subjects and 24=6*4 regressors. You need to add subjects or remove 
regressors (ie, classes or covariates)
doug

On 9/18/13 11:41 AM, Robert Schulz wrote:
 Hello,

 I am using mri_glmfit to perform a correlation analysis between some
 surface-based DTI measures and a behavioural outcome (grip), aiming to
 correct for scannertyp (C,I,W), handedness (R,L) as discrete variables and
 age (AGE) and duration (Mo) as continuous covariates. Please find the fsgd
 file, the contrast file and the calculated Xg down below.
 However, I get the follow error:

 DOF = -10
 ERROR: DOF = -10 (the complete output is attached)

 I would be grateful if somebody could help. I already tried it with demeaned
 data, z-transformed data, it doesn't help.

 Thank you for your help,

 Robert


 

 fsgd file:
 GroupDescriptorFile 1
 Title OSGM
 Class CR
 Class CL
 Class WL
 Class WR
 Class IR
 Class IL
 Variables Age Mo Grip
 Input c02 CR 52 85 0.250
 Input c04 CR 71 27 0.652
 Input c05 CL 63 12 0.788
 Input c06 WL 77 26 0.438
 Input c07 WR 61 13 0.717
 Input c10 IR 68 9 0.730
 Input c11 IL 63 13 0.934
 Input c12 IL 29 12 1.170
 Input c13 IR 46 12 0.964
 Input c14 IR 75 14 0.655
 Input c15 IL 68 13 1.098
 Input c16 IR 69 12 1.028
 Input c18 WL 40 20 0.698
 Input c19 WL 53 13 0.547

 contrast file:
 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1

 design matrix:

 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +52.0 +0.0
 +0.0 +0.0 +0.0 +0.0 +85.0 +0.0 +0.0 +0.0
 +0.0 +0.0 +0.25000 +0.0 +0.0 +0.0 +0.0 +0.0
 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +71.0 +0.0
 +0.0 +0.0 +0.0 +0.0 +27.0 +0.0 +0.0 +0.0
 +0.0 +0.0 +0.65200 +0.0 +0.0 +0.0 +0.0 +0.0
 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0 +63.0
 +0.0 +0.0 +0.0 +0.0 +0.0 +12.0 +0.0 +0.0
 +0.0 +0.0 +0.0 +0.78800 +0.0 +0.0 +0.0 +0.0
 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0
 +77.0 +0.0 +0.0 +0.0 +0.0 +0.0 +26.0 +0.0
 +0.0 +0.0 +0.0 +0.0 +0.43800 +0.0 +0.0 +0.0
 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0
 +0.0 +61.0 +0.0 +0.0 +0.0 +0.0 +0.0 +13.0
 +0.0 +0.0 +0.0 +0.0 +0.0 +0.71700 +0.0 +0.0
 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0
 +0.0 +0.0 +68.0 +0.0 +0.0 +0.0 +0.0 +0.0
 +9.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.73000 +0.0
 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0
 +0.0 +0.0 +0.0 +63.0 +0.0 +0.0 +0.0 +0.0
 +0.0 +13.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.93400
 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0
 +0.0 +0.0 +0.0 +29.0 +0.0 +0.0 +0.0 +0.0
 +0.0 +12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.17000
 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0
 +0.0 +0.0 +46.0 +0.0 +0.0 +0.0 +0.0 +0.0
 +12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.96400 +0.0
 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0
 +0.0 +0.0 +75.0 +0.0 +0.0 +0.0 +0.0 +0.0
 +14.0 +0.0 +0.0 +0.0 +0.0 +0.0 +0.65500 +0.0
 +0.0 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0
 +0.0 +0.0 +0.0 +68.0 +0.0 +0.0 +0.0 +0.0
 +0.0 +13.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.09800
 +0.0 +0.0 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0
 +0.0 +0.0 +69.0 +0.0 +0.0 +0.0 +0.0 +0.0
 +12.0 +0.0 +0.0 +0.0 +0.0 +0.0 +1.02800 +0.0
 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0
 +40.0 +0.0 +0.0 +0.0 +0.0 +0.0 +20.0 +0.0
 +0.0 +0.0 +0.0 +0.0 +0.69800 +0.0 +0.0 +0.0
 +0.0 +0.0 +1.0 +0.0 +0.0 +0.0 +0.0 +0.0
 +53.0 +0.0 +0.0 +0.0 +0.0 +0.0 +13.0 +0.0
 +0.0 +0.0 +0.0 +0.0 +0.54700 +0.0 +0.0 +0.0

 output:

 gdfReadHeader: reading
 /home/schulz/dti/premotorstroke/wm-probe/fs_no3/glmout_corr_l/glmout/corr.fsgd
 INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done.
 Continuous Variable Means (all subjects)
 0 Age 59.6429 13.4462
 1 Mo 20.0714 18.7444
 2 Grip 0.762071 0.248599
 Class Means of each Continuous Variable
 1 CR 61.5000 56. 

[Freesurfer] mri_glmfit error with design matix

[Sinead Kelly]

Dear Members,

I am using mri_glmfit for the first time with the .fsgd file below,
however, I am receiving the following error: ERROR: matrix is
ill-conditioned or badly scaled, condno = 1e+08

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

I have also pasted the design matrix below as I cannot figure out what is
wrong with it. I would really appreciate if anyone could help me this
issue. Also note that I am running this for just a subset of my total data
set as a test before I run it on my full data set.

Thank you very much for your help,

Sinead

GroupDescriptorFile 1
Title MIR137
Class TGFemale
Class TGMale
Class TTFemale
Class TTMale

Variables Age
Input CON3140/001 TGFemale 37
Input CON3891/001 TTFemale 33
Input CON4664/001 TTFemale 40
Input CON5591/001 TTMale   41
Input CON7009/001 TGMale   21
Input CON7024/001 TTMale   59
Input CON7038/001 TTMale   56
Input CON7050/001 TTMale   30
Input CON7054/001 TTMale   43
Input CON7055/001 TTMale   43
Input CON7072/001 TTFemale 41
Input CON7082/001 TTFemale 29
Input CON7087/001 TTFemale 23
Input CON7090/001 TGFemale 59
Input CON7092/001 TTFemale 21
Input CON9004/001 TGFemale 28
Input CON9009/001 TTMale   42
Input CON9040/001 TTMale 56
Input CON9064/001 TTMale 55
Input CON9069/001 TGFemale 54
Input CON9070/001 TTFemale 55
Input CON9081/001 TTFemale 50
Input CON9091/001 TTMale 27
Input CON9093/001 TTMale 54
DefaultVariable Age

Normalized matrix condition is 1e+08
Design matrix --
 1.000   0.000   0.000   0.000   37.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   33.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   40.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   41.000;
 0.000   1.000   0.000   0.000   0.000   21.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   59.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   56.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   30.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   43.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   43.000;
 0.000   0.000   1.000   0.000   0.000   0.000   41.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   29.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   23.000   0.000;
 1.000   0.000   0.000   0.000   59.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   21.000   0.000;
 1.000   0.000   0.000   0.000   28.000   0.000   0.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   42.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   56.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   55.000;
 1.000   0.000   0.000   0.000   54.000   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   55.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   50.000   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   27.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   54.000;


-- 
Sinead Kelly
Neuropsychiatric Genetics Group
Trinity Centre
St. James's Hospital
Dublin 8
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Re: [Freesurfer] mri_glmfit error with design matix

[Douglas N Greve]

Hi sinead, you only have one TGMale. You can't fit aslope and intercept 
to a single point!
doug


On 05/15/2013 11:40 AM, Sinead Kelly wrote:
 Dear Members,

 I am using mri_glmfit for the first time with the .fsgd file below, 
 however, I am receiving the following error: ERROR: matrix is 
 ill-conditioned or badly scaled, condno = 1e+08
 
 Possible problem with experimental design:
 Check for duplicate entries and/or lack of range of
 continuous variables within a class.

 I have also pasted the design matrix below as I cannot figure out what 
 is wrong with it. I would really appreciate if anyone could help me 
 this issue. Also note that I am running this for just a subset of my 
 total data set as a test before I run it on my full data set.

 Thank you very much for your help,

 Sinead

 GroupDescriptorFile 1
 Title MIR137
 Class TGFemale
 Class TGMale
 Class TTFemale
 Class TTMale

 Variables Age
 Input CON3140/001 TGFemale 37
 Input CON3891/001 TTFemale 33
 Input CON4664/001 TTFemale 40
 Input CON5591/001 TTMale 41
 Input CON7009/001 TGMale 21
 Input CON7024/001 TTMale 59
 Input CON7038/001 TTMale 56
 Input CON7050/001 TTMale 30
 Input CON7054/001 TTMale 43
 Input CON7055/001 TTMale 43
 Input CON7072/001 TTFemale 41
 Input CON7082/001 TTFemale 29
 Input CON7087/001 TTFemale 23
 Input CON7090/001 TGFemale 59
 Input CON7092/001 TTFemale 21
 Input CON9004/001 TGFemale 28
 Input CON9009/001 TTMale 42
 Input CON9040/001 TTMale 56
 Input CON9064/001 TTMale 55
 Input CON9069/001 TGFemale 54
 Input CON9070/001 TTFemale 55
 Input CON9081/001 TTFemale 50
 Input CON9091/001 TTMale 27
 Input CON9093/001 TTMale 54
 DefaultVariable Age

 Normalized matrix condition is 1e+08
 Design matrix --
  1.000   0.000   0.000   0.000   37.000   0.000   0.000 0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   33.000 0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   40.000 0.000;
  0.000   0.000   0.000   1.000   0.000   0.000   0.000 41.000;
  0.000   1.000   0.000   0.000   0.000   21.000   0.000 0.000;
  0.000   0.000   0.000   1.000   0.000   0.000   0.000 59.000;
  0.000   0.000   0.000   1.000   0.000   0.000   0.000 56.000;
  0.000   0.000   0.000   1.000   0.000   0.000   0.000 30.000;
  0.000   0.000   0.000   1.000   0.000   0.000   0.000 43.000;
  0.000   0.000   0.000   1.000   0.000   0.000   0.000 43.000;
  0.000   0.000   1.000   0.000   0.000   0.000   41.000 0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   29.000 0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   23.000 0.000;
  1.000   0.000   0.000   0.000   59.000   0.000   0.000 0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   21.000 0.000;
  1.000   0.000   0.000   0.000   28.000   0.000   0.000 0.000;
  0.000   0.000   0.000   1.000   0.000   0.000   0.000 42.000;
  0.000   0.000   0.000   1.000   0.000   0.000   0.000 56.000;
  0.000   0.000   0.000   1.000   0.000   0.000   0.000 55.000;
  1.000   0.000   0.000   0.000   54.000   0.000   0.000 0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   55.000 0.000;
  0.000   0.000   1.000   0.000   0.000   0.000   50.000 0.000;
  0.000   0.000   0.000   1.000   0.000   0.000   0.000 27.000;
  0.000   0.000   0.000   1.000   0.000   0.000   0.000 54.000;


 -- 
 Sinead Kelly
 Neuropsychiatric Genetics Group
 Trinity Centre
 St. James's Hospital
 Dublin 8


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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
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Fax: 617-726-7422

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[Freesurfer] mri_glmfit error

[YUMI MAEDA]

HI,
I am trying to see difference in groupmap between 2 time-point within 1
group with glmfit.

I followed the instructionPairedAnalysis.
mris_preproc  --paired-diff

mri_glmfit --surf fsaverage $hemi
--y $hemi_cope1_$grp.sm$fwhmsrc.mgh
--yffxvar $hemi_varcope1_$grp.sm$fwhmsrc.mgh
--glmdir $fsdir/group_surf//$hemi_cope$num_$grp.sm$fwhmsrc_ffx
--ffxdof 1872 --osgm

When I checked the output of the mri_glmfit, the mask file does not cover
the entire brain as the cope/varcope does. it is much smaller and missing
parietal brain.

the log file says Reshaping mriglm-mask...
Is this the issue?

YUMI




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[Freesurfer] mri_glmfit error

[kelsi]

Hi Freesurfers,

I am having problems with mri_glmfit.  I am doing a one sample ttest with
thickness values.  However, when i enter -surf Subject1 lh
thickness.fsaverage.mgh, I receive an error message saying that the
surface could not be opened.  The path is correct and I entered setenv
SUBJECTS_DIR ./ in my directory before running the glm.  How would I fix
this error?  Thank you!

Kelsi Hirai
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[Freesurfer] Mri_glmfit ERROR: dimension inconsistency in source data

[Agnieszka Burzynska]

Hi,
During running fixed effects glm to combine runs, the analysis of all but
one subject went fine.

The log file contains this error message:
mri_surf2surf --srcsubject 1250 --srchemi lh --srcsurfreg sphere.reg
--trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval
3runs/tmp.mris_preproc.63877/1250.1.mgh --sval
3runs/tmp.mris_preproc.63877/subjsurfvals.mgh --noreshape --no-cortex
ERROR: dimension inconsistency in source data
   Number of surface vertices = 132315
   Number of value vertices = 132299

I see that mri_vol2surf --src run1.feat/stats/varcope1.nii.gz --srcreg
run1.feat/reg/freesurfer/anat2exf.register.dat --hemi lh --out
3runs/tmp.mris_preproc.63877/subjsurfvals.mgh --noreshape

Results in creating a file with dimensions 132299 1 1.

Which data source data has then 132315 vertices? How can I correct this?

Thank you for your help!

Best,
Aga



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Re: [Freesurfer] mri_glmfit error

[Rafa x]

Dear Doug I’ve tried runnig the command:

mri_glmfit-sim --glmdir lh.fsgd_subj_gauss001 --sim mc-z 625 2.3013
mc-z.pos.3 --sim-sign pos

And the following error appears:
ERROR: desig matrix is not orthogonal, cannot be used with permutation.

As I’ve search in the forum list, I have found that the --sim perm
option does not work with continuous variables, but that --sim mc-z
does, which are the differences between this two methods?

Bests,
Rafa.


2011/1/26 Douglas N Greve gr...@nmr.mgh.harvard.edu:
 For the permutation sim, the fwhm should be set to 0. Why are you not using
 mri_glmfit-sim? I would strongly recommend it as that will make sure that
 all the arguments are correct.

 doug

 Rafa x wrote:

 Dear Freesurfers,
 In Freesurfer v5.0 when I try to run the command:

 mri_glmfit --surf CNTRL_MCI_RAFA_average lh --C contrast.mat --fsgd
 fsgd.txt dods --mask lh.fsgd_subj/mask.mgh --y
 CNTRL_MCI_RAFA_stats/lh.fsgd_subj.mgh --sim perm 625 2.301 csd1
 --sim-sign pos --seed 6555731749

 I always get the following error:

 ERROR: you must supply --fwhm with --sim, even if it is 0

 Is there a bug in the mri_glmfit function?

 Thank you all in advance,
 Rafael.
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 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer




 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html



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 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
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 but does not contain patient information, please contact the sender and
 properly
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Re: [Freesurfer] mri_glmfit error

[Douglas N Greve]

That command would be for an mc-z simlation, not a permutation. But you 
are right the perm does not allow non-orthogonal matrices. The mc-z 
synthesizes a z-field, smooths it, thresholds it, and extracts clusters, 
repeats this 1 times to get an idea of what cluster sizes should be 
expected under the null. Permutation randomly changes the rows of the 
design matrix, runs the analysis, gets a z-map, thresholds it, and 
extracts clusters, repeats this 1 times to get an idea of what 
cluster sizes should be expected under the permutation null.

doug

Rafa x wrote:
 Dear Doug I’ve tried runnig the command:

 mri_glmfit-sim --glmdir lh.fsgd_subj_gauss001 --sim mc-z 625 2.3013
 mc-z.pos.3 --sim-sign pos

 And the following error appears:
 ERROR: desig matrix is not orthogonal, cannot be used with permutation.

 As I’ve search in the forum list, I have found that the --sim perm
 option does not work with continuous variables, but that --sim mc-z
 does, which are the differences between this two methods?

 Bests,
 Rafa.


 2011/1/26 Douglas N Greve gr...@nmr.mgh.harvard.edu:
   
 For the permutation sim, the fwhm should be set to 0. Why are you not using
 mri_glmfit-sim? I would strongly recommend it as that will make sure that
 all the arguments are correct.

 doug

 Rafa x wrote:
 
 Dear Freesurfers,
 In Freesurfer v5.0 when I try to run the command:

 mri_glmfit --surf CNTRL_MCI_RAFA_average lh --C contrast.mat --fsgd
 fsgd.txt dods --mask lh.fsgd_subj/mask.mgh --y
 CNTRL_MCI_RAFA_stats/lh.fsgd_subj.mgh --sim perm 625 2.301 csd1
 --sim-sign pos --seed 6555731749

 I always get the following error:

 ERROR: you must supply --fwhm with --sim, even if it is 0

 Is there a bug in the mri_glmfit function?

 Thank you all in advance,
 Rafael.
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



   
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358 Fax: 617-726-7422

 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html



 The information in this e-mail is intended only for the person to whom it is
 addressed. If you believe this e-mail was sent to you in error and the
 e-mail
 contains patient information, please contact the Partners Compliance
 HelpLine at
 http://www.partners.org/complianceline . If the e-mail was sent to you in
 error
 but does not contain patient information, please contact the sender and
 properly
 dispose of the e-mail.


 


   

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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[Freesurfer] mri_glmfit error

[Rafa x]

Dear Freesurfers,
In Freesurfer v5.0 when I try to run the command:

mri_glmfit --surf CNTRL_MCI_RAFA_average lh --C contrast.mat --fsgd
fsgd.txt dods --mask lh.fsgd_subj/mask.mgh --y
CNTRL_MCI_RAFA_stats/lh.fsgd_subj.mgh --sim perm 625 2.301 csd1
--sim-sign pos --seed 6555731749

I always get the following error:

ERROR: you must supply --fwhm with --sim, even if it is 0

Is there a bug in the mri_glmfit function?

Thank you all in advance,
Rafael.
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_glmfit error

[Douglas N Greve]

For the permutation sim, the fwhm should be set to 0. Why are you not 
using mri_glmfit-sim? I would strongly recommend it as that will make 
sure that all the arguments are correct.

doug

Rafa x wrote:
 Dear Freesurfers,
 In Freesurfer v5.0 when I try to run the command:

 mri_glmfit --surf CNTRL_MCI_RAFA_average lh --C contrast.mat --fsgd
 fsgd.txt dods --mask lh.fsgd_subj/mask.mgh --y
 CNTRL_MCI_RAFA_stats/lh.fsgd_subj.mgh --sim perm 625 2.301 csd1
 --sim-sign pos --seed 6555731749

 I always get the following error:

 ERROR: you must supply --fwhm with --sim, even if it is 0

 Is there a bug in the mri_glmfit function?

 Thank you all in advance,
 Rafael.
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


   

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.