Re: [Freesurfer] lh.thickness can not found

[Fischl, Bruce]

You need to tell recon-all what to do. Try adding -all at the end
On Nov 11, 2021, at 10:33 PM, a Chinese reader  wrote:



External Email - Use Caution

Hello FreeSurfer Developers,

I'm attempting to compute the thickness of the grey matter ,but for some of my 
subjects I get the following error when I run the recon-all -s <> -all command:

Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.


I've searched the list and no similar errors have been reported. Did this 
warning have any effect for my outcome?And why my lh.thickness cannot 
generated? Does anyone have any thoughts on how to trouble-shoot this one? 
Also, Ive attached the recon-all.log in case it's of any use.


Best regards,
Zhang Xia















___
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
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 http://www.massgeneralbrigham.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.
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] permutation simulation errror

[Douglas N. Greve]

ok, that is the problem. What computer platform are you using and which 
version of FS do you have?


On 11/11/2021 6:42 PM, Brown, Alexander wrote:


External Email - Use Caution

< stem2fname /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres
ERROR: could not determine file for 
/home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres >


Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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


*Sent:* Thursday, November 11, 2021 5:39 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] permutation simulation errror
What do you get if you run
stem2fname /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres
?

On 11/11/2021 6:35 PM, Brown, Alexander wrote:


External Email - Use Caution

See attached.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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

*Sent:* Thursday, November 11, 2021 3:46 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 

*Subject:* Re: [Freesurfer] permutation simulation errror
OK, can you run mri_glmfit-sim with --debug as the first option and 
send me the output?


On 11/11/2021 4:08 PM, Brown, Alexander wrote:


External Email - Use Caution

Hi,

Yes, see attached.

-Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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

*Sent:* Thursday, November 11, 2021 3:05 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 

*Subject:* Re: [Freesurfer] permutation simulation errror
What are the contents of 
/home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled? Can you send me 
the ls of it?


On 11/11/2021 3:38 PM, Brown, Alexander wrote:


External Email - Use Caution

Hi,

Now attached is the mri_glmfit-sim terminal output. the only output 
is the error message.


Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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


*Sent:* Thursday, November 11, 2021 2:27 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 


*Subject:* Re: [Freesurfer] permutation simulation errror
That is for mri_glmfit, not mri_glmfit-sim.

On 11/11/2021 3:24 PM, Brown, Alexander wrote:


External Email - Use Caution

Yes, please see the attached text file.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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


*Sent:* Thursday, November 11, 2021 2:04 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 


*Subject:* Re: [Freesurfer] permutation simulation errror
Can you capture and send the full terminal output from mri_glmfit-sim?

On 11/10/2021 10:41 PM, Brown, Alexander wrote:


External Email - Use Caution

Hi Dr. Greve,

I am using FS 6.0 on Ubuntu 18.04.

Unfortunately, no mri_glmfit-sim log file is generated when I 
attempt to run mri_glmfit-sim.


Best,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

*From:* freesurfer-boun...@nmr.mgh.harvard.

Re: [Freesurfer] permutation simulation errror

[Brown, Alexander]

External Email - Use Caution

< stem2fname /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres
ERROR: could not determine file for 
/home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres >

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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

Sent: Thursday, November 11, 2021 5:39 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] permutation simulation errror

What do you get if you run
stem2fname /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres
?

On 11/11/2021 6:35 PM, Brown, Alexander wrote:

External Email - Use Caution

See attached.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Thursday, November 11, 2021 3:46 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] permutation simulation errror

OK, can you run mri_glmfit-sim with --debug as the first option and send me the 
output?

On 11/11/2021 4:08 PM, Brown, Alexander wrote:

External Email - Use Caution

Hi,

Yes, see attached.

-Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Thursday, November 11, 2021 3:05 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] permutation simulation errror

What are the contents of  /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled? Can 
you send me the ls of it?

On 11/11/2021 3:38 PM, Brown, Alexander wrote:

External Email - Use Caution

Hi,

Now attached is the mri_glmfit-sim terminal output. the only output is the 
error message.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Thursday, November 11, 2021 2:27 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] permutation simulation errror

That is for mri_glmfit, not mri_glmfit-sim.

On 11/11/2021 3:24 PM, Brown, Alexander wrote:

External Email - Use Caution

Yes, please see the attached text file.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Thursday, November 11, 2021 2:04 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] permutation simulation errror

Can you capture and send the full terminal output from mri_glmfit-sim?

On 11/10/2021 10:41 PM, Brown, Alexander wrote:

External Email - Use Caution

Hi Dr. Greve,

I am using FS 6.0 on Ubuntu 18.04.

Unfortunately, no mri_glmfit-sim log file is generated when I attempt to run 
mri_glmfit-sim.

Best,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Wednesday, November 10, 2021 4:40 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] permutation simulation errror

WARNING: This message has originated from an External Source. This may be a 
phish

Re: [Freesurfer] permutation simulation errror

[Douglas N. Greve]

What do you get if you run
stem2fname /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres
?

On 11/11/2021 6:35 PM, Brown, Alexander wrote:


External Email - Use Caution

See attached.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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


*Sent:* Thursday, November 11, 2021 3:46 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] permutation simulation errror
OK, can you run mri_glmfit-sim with --debug as the first option and 
send me the output?


On 11/11/2021 4:08 PM, Brown, Alexander wrote:


External Email - Use Caution

Hi,

Yes, see attached.

-Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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

*Sent:* Thursday, November 11, 2021 3:05 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 

*Subject:* Re: [Freesurfer] permutation simulation errror
What are the contents of  
/home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled? Can you send me the 
ls of it?


On 11/11/2021 3:38 PM, Brown, Alexander wrote:


External Email - Use Caution

Hi,

Now attached is the mri_glmfit-sim terminal output. the only output 
is the error message.


Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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

*Sent:* Thursday, November 11, 2021 2:27 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 

*Subject:* Re: [Freesurfer] permutation simulation errror
That is for mri_glmfit, not mri_glmfit-sim.

On 11/11/2021 3:24 PM, Brown, Alexander wrote:


External Email - Use Caution

Yes, please see the attached text file.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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


*Sent:* Thursday, November 11, 2021 2:04 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 


*Subject:* Re: [Freesurfer] permutation simulation errror
Can you capture and send the full terminal output from mri_glmfit-sim?

On 11/10/2021 10:41 PM, Brown, Alexander wrote:


External Email - Use Caution

Hi Dr. Greve,

I am using FS 6.0 on Ubuntu 18.04.

Unfortunately, no mri_glmfit-sim log file is generated when I 
attempt to run mri_glmfit-sim.


Best,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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


*Sent:* Wednesday, November 10, 2021 4:40 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 


*Subject:* Re: [Freesurfer] permutation simulation errror
WARNING: This message has originated from an External Source. This 
may be a phishing expedition that can result in unauthorized 
access to our IT System. Please use proper judgment and caution 
when opening attachments, clicking links, or responding to this email.
Which version of FS are you using? Can you send the log file 
created by mri_glmfit-sim (different than the one you sent)?


On 11/10/2021 3:49 PM, Brown, Alexander wrote:


External Email - Use Caution

Hello,

I am attempting to run a permutation simulation to correct for 
multiple comparisons and am getting the following error:


< mri_glmfit-sim

Re: [Freesurfer] permutation simulation errror

[Brown, Alexander]

External Email - Use Caution

See attached.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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

Sent: Thursday, November 11, 2021 3:46 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] permutation simulation errror

OK, can you run mri_glmfit-sim with --debug as the first option and send me the 
output?

On 11/11/2021 4:08 PM, Brown, Alexander wrote:

External Email - Use Caution

Hi,

Yes, see attached.

-Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Thursday, November 11, 2021 3:05 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] permutation simulation errror

What are the contents of  /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled? Can 
you send me the ls of it?

On 11/11/2021 3:38 PM, Brown, Alexander wrote:

External Email - Use Caution

Hi,

Now attached is the mri_glmfit-sim terminal output. the only output is the 
error message.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Thursday, November 11, 2021 2:27 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] permutation simulation errror

That is for mri_glmfit, not mri_glmfit-sim.

On 11/11/2021 3:24 PM, Brown, Alexander wrote:

External Email - Use Caution

Yes, please see the attached text file.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Thursday, November 11, 2021 2:04 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] permutation simulation errror

Can you capture and send the full terminal output from mri_glmfit-sim?

On 11/10/2021 10:41 PM, Brown, Alexander wrote:

External Email - Use Caution

Hi Dr. Greve,

I am using FS 6.0 on Ubuntu 18.04.

Unfortunately, no mri_glmfit-sim log file is generated when I attempt to run 
mri_glmfit-sim.

Best,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Wednesday, November 10, 2021 4:40 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] permutation simulation errror

WARNING: This message has originated from an External Source. This may be a 
phishing expedition that can result in unauthorized access to our IT System. 
Please use proper judgment and caution when opening attachments, clicking 
links, or responding to this email.
Which version of FS are you using? Can you send the log file created by 
mri_glmfit-sim (different than the one you sent)?

On 11/10/2021 3:49 PM, Brown, Alexander wrote:

External Email - Use Caution

Hello,

I am attempting to run a permutation simulation to correct for multiple 
comparisons and am getting the following error:

< mri_glmfit-sim --glmdir /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled 
--perm 1000 1.3 neg --perm-resid
ERROR: cannot find residual 
/home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres needed with --perm-resid
  when running mri_glmfit, make sure to include --eres-save >

Attached is the mri glmfit log. I ran the command with the --eres-save flag, 
and the eres.mgh file is generated in the glm directory.

I have downloaded

Re: [Freesurfer] permutation simulation errror

[Douglas N. Greve]

OK, can you run mri_glmfit-sim with --debug as the first option and send 
me the output?


On 11/11/2021 4:08 PM, Brown, Alexander wrote:


External Email - Use Caution

Hi,

Yes, see attached.

-Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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


*Sent:* Thursday, November 11, 2021 3:05 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] permutation simulation errror
What are the contents of 
/home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled? Can you send me the 
ls of it?


On 11/11/2021 3:38 PM, Brown, Alexander wrote:


External Email - Use Caution

Hi,

Now attached is the mri_glmfit-sim terminal output. the only output 
is the error message.


Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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

*Sent:* Thursday, November 11, 2021 2:27 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 

*Subject:* Re: [Freesurfer] permutation simulation errror
That is for mri_glmfit, not mri_glmfit-sim.

On 11/11/2021 3:24 PM, Brown, Alexander wrote:


External Email - Use Caution

Yes, please see the attached text file.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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

*Sent:* Thursday, November 11, 2021 2:04 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 

*Subject:* Re: [Freesurfer] permutation simulation errror
Can you capture and send the full terminal output from mri_glmfit-sim?

On 11/10/2021 10:41 PM, Brown, Alexander wrote:


External Email - Use Caution

Hi Dr. Greve,

I am using FS 6.0 on Ubuntu 18.04.

Unfortunately, no mri_glmfit-sim log file is generated when I 
attempt to run mri_glmfit-sim.


Best,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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


*Sent:* Wednesday, November 10, 2021 4:40 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 


*Subject:* Re: [Freesurfer] permutation simulation errror
WARNING: This message has originated from an External Source. This 
may be a phishing expedition that can result in unauthorized access 
to our IT System. Please use proper judgment and caution when 
opening attachments, clicking links, or responding to this email.
Which version of FS are you using? Can you send the log file 
created by mri_glmfit-sim (different than the one you sent)?


On 11/10/2021 3:49 PM, Brown, Alexander wrote:


External Email - Use Caution

Hello,

I am attempting to run a permutation simulation to correct for 
multiple comparisons and am getting the following error:


< mri_glmfit-sim --glmdir 
/home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled --perm 1000 1.3 
neg --perm-resid
ERROR: cannot find residual 
/home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres needed with 
--perm-resid

  when running mri_glmfit, make sure to include --eres-save >

Attached is the mri glmfit log. I ran the command with the 
--eres-save flag, and the eres.mgh file is generated in the glm 
directory.


I have downloaded the patch and have run this style of analysis 
multiple times without issue until today.


I appreciate any help!

Please let me know if you need any additional information.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu  

Re: [Freesurfer] question regarding FSGD file for coding discrete regressors

[Zeng, Qi]

External Email - Use Caution

For example, if my Class CaseFemaleNonWhite has no subject, should I cancel
the contrast between CaseFemaleNonWhite vs ControlFemaleNonWhite?
However, that will leave my ControlFemaleNonWhite subjects unrecognized? Or
it is better to cancel the race discrete as covariates?

Best,
Zeng


On Thu, Nov 11, 2021 at 4:07 PM Zeng, Qi  wrote:

> got you, thanks
>
> Best,
> Zeng
>
>
>
> On Thu, Nov 11, 2021 at 4:06 PM Douglas N. Greve 
> wrote:
>
>> For DODS you would add 16 zeros (8 classes times 2 continuous variables)
>>
>> On 11/11/2021 4:00 PM, Zeng, Qi wrote:
>>
>> External Email - Use Caution
>> So for the DODS case, is "1 -1 1 -1 1 -1 1 -1 0 0 0 0" for the following
>> FSGD:
>>
>> GroupDescriptorFile 1
>> Title MyStudy
>> Class CaseMaleWhite
>> Class ControlMaleWhite
>> Class CaseMaleNonWhite
>> Class ControlMaleNonWhite
>> Class CaseFemaleWhite
>> Class ControlFemaleWhite
>> Class CaseFemaleNonWhite
>> Class ControlFemaleNonWhite
>> Variables age_bl eTIV
>> Input Sub001_base ControlFemaleWhite 85 1350519.71
>> Input Sub002_base ControlFemaleWhite 81.3 1558515.86
>>
>> Best,
>> Qi
>>
>> On Thu, Nov 11, 2021 at 3:28 PM Douglas N. Greve 
>> wrote:
>>
>>> For the DOSS case, yes.
>>>
>>> On 11/11/2021 3:23 PM, Zeng, Qi wrote:
>>>
>>> External Email - Use Caution
>>> Hi  Douglas,
>>>
>>> If to set up the FSGD as below, is my design matrix for case and control
>>> comparison as "1 -1 1 -1 1 -1 1 -1 0 0"  ?
>>>
>>> GroupDescriptorFile 1
>>> Title MyStudy
>>> Class CaseMaleWhite
>>> Class ControlMaleWhite
>>> Class CaseMaleNonWhite
>>> Class ControlMaleNonWhite
>>> Class CaseFemaleWhite
>>> Class ControlFemaleWhite
>>> Class CaseFemaleNonWhite
>>> Class ControlFemaleNonWhite
>>> VariablesAge eTIV
>>> Input Sub001_base  Control   Female  White   85 1350519.71
>>> Input Sub002_base  Control   Female  White   81.3   1558515.86
>>>
>>> Best,
>>> Qi
>>>
>>> On Thu, Nov 11, 2021 at 3:06 PM Douglas N. Greve 
>>> wrote:
>>>
 I would advice setting up the FSGD files with 8 classes based on your 3
 discrete, 2-level variables, eg, MaleControlWhite then use two continuous
 variables Age and eTIV.
 You should definitely normalize the eTIV (and probably age too)

 On 11/10/2021 7:07 PM, Zeng, Qi wrote:

 External Email - Use Caution
 Hi Douglas,

 Just to be clear, should I recode discrete variables as numeric as
 sample1) or change discrete variables into strings 2) or even change the
 comparison groups into strings too 3)?
 1)
 Variables Age Gender Race eTIV
 Input Sub001_base Control 85 1 1 1350519.71
 Input Sub002_base Control 81.3   0 1 1558515.86
 Input Sub003_base Control 81.3   0 0 1558515.86

 or 2)
 Variables Age Gender Race eTIV
 Input Sub001_base Control 85 "Female" "White" 1350519.71
 Input Sub002_base Control 81.3  "Male" "White" 1558515.86
 Input Sub003_base Control 72.7  "Male" "White" 1187649.47

 or 3)
 Variables  Age Gender Race eTIV
 Input Sub001_base "Control" 85 "Female" "White" 1350519.71
 Input Sub002_base "Control" 81.3  "Male" "White" 1558515.86
 Input Sub003_base "Control" 72.7  "Male" "White" 1187649.47


 Best,
 Zeng



 On Wed, Nov 10, 2021 at 6:38 PM Douglas N. Greve <
 dgr...@mgh.harvard.edu> wrote:

> Did you read the error message? It says:
> Variable 2 has character string Female
> Variables should be continuous numbers
> You have listed Gender and Race as strings, they have to be numbers
> (eg, 1, 2)
> You probably want to have these be discrete variables instead of
> continuous
>
> On 11/10/2021 6:20 PM, Zeng, Qi wrote:
>
> External Email - Use Caution
> Hi Douglas,
>
> Here is the command line:
> mri_glmfit \
>   --y rh.thickness-rate.MyStudy.10.mgh \
>   --fsgd FSGD/MyStudy.fsgd dods\
>   --C Contrasts/Case-Control_age_gender_race_etiv.mtx\
>   --surf fsaverage rh \
>   --cortex \
>   --glmdir
> rh.thickness-rate.MyStudy.10.mgh_age_gender_race_etiv.glmdir \
>   --eres-save
>
> Also error message in terminal:
> gdfRead(): reading FSGD/MyStudy.fsgd
> WARNING: variable 1 is "Gender" which is often a discrete factor
>   The proper way to handle discrete factors is to create classes.
>   See *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> https://secure-web.cisco.com/1c_MdQ5rEp7srI_kPpk4efkiqV9_OF913y30NhIzAsUQpPJT6D4K203HDfIxcL-TDH3c599tOGLbFE5W5-jbW8uvVJdfDK0NdK1oPqAiN9uQKK1ZW7SeFpLOgiWdZCQ8HxdK1UFbkK0Q3Vx_JHHPqlqjz8VZPupNVKt8xNZeLTNDuer9_aUm4HCa3ata1caUSeaFn-XV12g2KJgkoooe3dFA6jAMZuiwZQZt2DUIIbPQaQh5Q2PdYbv_fDaPGvJH-nJAbgu_Y77xOlBpuzquWrQmko9t99kQiDrRPjkeAcupXcjwIuTly8THZ3i-OYDIV/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
> 

Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats

[Castro Leal, Gonzalo]

External Email - Use Caution

Thanks for the effort. I assumed that since this was data was from a study, it 
could be used in Freesurfer. Good to know from now on.

Many thanks,
Gonzalo.

De: freesurfer-boun...@nmr.mgh.harvard.edu 
 en nombre de Douglas N. Greve 

Enviado: jueves, 11 de noviembre de 2021 20:25
Para: freesurfer@nmr.mgh.harvard.edu 
Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats

I looked at your data. The problem is that the T2-pial placement is not very 
good.  In some places it is much thinner, in some places it it somewhat 
thicker. This makes the volume computation a little unpredictable (can't just 
assume that average thickenss*area will give  you a reasonable value). The 
T2-pial is not placed well because the T2 is very low resolution (3mm slice 
thickness); it is hard to determine the boundaries of a 2-3mm structure when 
your slices are 3mm


On 11/10/2021 10:55 AM, Castro Leal, Gonzalo wrote:

External Email - Use Caution

I have tried, but I get the following error:

local: Gonzalo_ADNI_sub-020S0899_T2.tar.gz remote: 
Gonzalo_ADNI_sub-020S0899_T2.tar.gz
421 Service not available, remote server has closed connection



De: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 en nombre de Douglas N. Greve 

Enviado: miércoles, 10 de noviembre de 2021 15:09
Para: freesurfer@nmr.mgh.harvard.edu 

Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats

Ah, I see. Can you upload those two subjects using the method below?

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.


On 11/10/2021 9:33 AM, Castro Leal, Gonzalo wrote:

External Email - Use Caution

Sorry I did not explain myself well. For some regions of the brain this is what 
happens:

Region 
Num Vertices   Surf AreaGrayVol   ThickAvg

lateralorbitofrontal 2969   2085   5489  2.469

lateralorbitofrontal 2969   2085   5173  2.566

The first one corresponds to T1 only and the second one to T1 plus T2 
processing. The surface measurement is the same (this happens for all regions) 
however the volume decreases while the thickness increases, which is why I am 
confused.

PD: the last mail was sent by mistake, sorry for the spam.

Many thanks,
Gonzalo.

De: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 en nombre de Douglas N. Greve 

Enviado: martes, 9 de noviembre de 2021 20:13
Para: freesurfer@nmr.mgh.harvard.edu 

Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats

In your first post, you said that you were confused as to why the thickness and 
volume were changing but the surface was not changing. Then you said that the 
pial surface changed. Does that answer your first question?

On 11/9/2021 1:33 PM, Castro Leal, Gonzalo wrote:

External Email - Use Caution

The time of the aparc.stats is 1h and 20min after the modification of the file 
pial.T2, and in the case of the T1 only processing the time stamp on the 
apar.stats is 20 min after the modification of the pial.T1. Does this answer 
your question or should I look into something else?

De: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 en nombre de Douglas N. Greve 

Enviado: martes, 9 de noviembre de 2021 18:09
Para: freesurfer@nmr.mgh.harvard.edu 

Asunto: Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats

Were the stats files regenerated? Check the modification date

On 11/9/2021 10:41 AM, Castro Leal, Gonzalo wrote:

External Email - Use Caution

Yes the pial surface changed and the white did not.

De: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 en nombre de Douglas N. Greve 

Enviado: martes, 9 de noviembre de 2021 14:49
Para: fre

Re: [Freesurfer] permutation simulation errror

[Brown, Alexander]

External Email - Use Caution

Hi,

Yes, see attached.

-Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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

Sent: Thursday, November 11, 2021 3:05 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] permutation simulation errror

What are the contents of  /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled? Can 
you send me the ls of it?

On 11/11/2021 3:38 PM, Brown, Alexander wrote:

External Email - Use Caution

Hi,

Now attached is the mri_glmfit-sim terminal output. the only output is the 
error message.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Thursday, November 11, 2021 2:27 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] permutation simulation errror

That is for mri_glmfit, not mri_glmfit-sim.

On 11/11/2021 3:24 PM, Brown, Alexander wrote:

External Email - Use Caution

Yes, please see the attached text file.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Thursday, November 11, 2021 2:04 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] permutation simulation errror

Can you capture and send the full terminal output from mri_glmfit-sim?

On 11/10/2021 10:41 PM, Brown, Alexander wrote:

External Email - Use Caution

Hi Dr. Greve,

I am using FS 6.0 on Ubuntu 18.04.

Unfortunately, no mri_glmfit-sim log file is generated when I attempt to run 
mri_glmfit-sim.

Best,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Wednesday, November 10, 2021 4:40 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] permutation simulation errror

WARNING: This message has originated from an External Source. This may be a 
phishing expedition that can result in unauthorized access to our IT System. 
Please use proper judgment and caution when opening attachments, clicking 
links, or responding to this email.
Which version of FS are you using? Can you send the log file created by 
mri_glmfit-sim (different than the one you sent)?

On 11/10/2021 3:49 PM, Brown, Alexander wrote:

External Email - Use Caution

Hello,

I am attempting to run a permutation simulation to correct for multiple 
comparisons and am getting the following error:

< mri_glmfit-sim --glmdir /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled 
--perm 1000 1.3 neg --perm-resid
ERROR: cannot find residual 
/home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres needed with --perm-resid
  when running mri_glmfit, make sure to include --eres-save >

Attached is the mri glmfit log. I ran the command with the --eres-save flag, 
and the eres.mgh file is generated in the glm directory.

I have downloaded the patch and have run this style of analysis multiple times 
without issue until today.

I appreciate any help!

Please let me know if you need any additional information.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/13RmTbMhlp4XCl9EabUEFlN7i4yzGBsdjfudfWPqwCiy8PAmPPagXbXymzQYfLOrg3g9Ktd0Ugjea6GfFa9AJB2s_PYe2RK0BrEVYKrbk0pXhYsgibwFpJ8ghTVaNZOHlXgIDPvuIEE1p7V83FzzYVYGTCn6e-uiimEhpBohuyqfheRRhY_zX9XauYb5FxJVbR4jtpc2a

Re: [Freesurfer] question regarding FSGD file for coding discrete regressors

[Zeng, Qi]

External Email - Use Caution

got you, thanks

Best,
Zeng



On Thu, Nov 11, 2021 at 4:06 PM Douglas N. Greve 
wrote:

> For DODS you would add 16 zeros (8 classes times 2 continuous variables)
>
> On 11/11/2021 4:00 PM, Zeng, Qi wrote:
>
> External Email - Use Caution
> So for the DODS case, is "1 -1 1 -1 1 -1 1 -1 0 0 0 0" for the following
> FSGD:
>
> GroupDescriptorFile 1
> Title MyStudy
> Class CaseMaleWhite
> Class ControlMaleWhite
> Class CaseMaleNonWhite
> Class ControlMaleNonWhite
> Class CaseFemaleWhite
> Class ControlFemaleWhite
> Class CaseFemaleNonWhite
> Class ControlFemaleNonWhite
> Variables age_bl eTIV
> Input Sub001_base ControlFemaleWhite 85 1350519.71
> Input Sub002_base ControlFemaleWhite 81.3 1558515.86
>
> Best,
> Qi
>
> On Thu, Nov 11, 2021 at 3:28 PM Douglas N. Greve 
> wrote:
>
>> For the DOSS case, yes.
>>
>> On 11/11/2021 3:23 PM, Zeng, Qi wrote:
>>
>> External Email - Use Caution
>> Hi  Douglas,
>>
>> If to set up the FSGD as below, is my design matrix for case and control
>> comparison as "1 -1 1 -1 1 -1 1 -1 0 0"  ?
>>
>> GroupDescriptorFile 1
>> Title MyStudy
>> Class CaseMaleWhite
>> Class ControlMaleWhite
>> Class CaseMaleNonWhite
>> Class ControlMaleNonWhite
>> Class CaseFemaleWhite
>> Class ControlFemaleWhite
>> Class CaseFemaleNonWhite
>> Class ControlFemaleNonWhite
>> VariablesAge eTIV
>> Input Sub001_base  Control   Female  White   85 1350519.71
>> Input Sub002_base  Control   Female  White   81.3   1558515.86
>>
>> Best,
>> Qi
>>
>> On Thu, Nov 11, 2021 at 3:06 PM Douglas N. Greve 
>> wrote:
>>
>>> I would advice setting up the FSGD files with 8 classes based on your 3
>>> discrete, 2-level variables, eg, MaleControlWhite then use two continuous
>>> variables Age and eTIV.
>>> You should definitely normalize the eTIV (and probably age too)
>>>
>>> On 11/10/2021 7:07 PM, Zeng, Qi wrote:
>>>
>>> External Email - Use Caution
>>> Hi Douglas,
>>>
>>> Just to be clear, should I recode discrete variables as numeric as
>>> sample1) or change discrete variables into strings 2) or even change the
>>> comparison groups into strings too 3)?
>>> 1)
>>> Variables Age Gender Race eTIV
>>> Input Sub001_base Control 85 1 1 1350519.71
>>> Input Sub002_base Control 81.3   0 1 1558515.86
>>> Input Sub003_base Control 81.3   0 0 1558515.86
>>>
>>> or 2)
>>> Variables Age Gender Race eTIV
>>> Input Sub001_base Control 85 "Female" "White" 1350519.71
>>> Input Sub002_base Control 81.3  "Male" "White" 1558515.86
>>> Input Sub003_base Control 72.7  "Male" "White" 1187649.47
>>>
>>> or 3)
>>> Variables  Age Gender Race eTIV
>>> Input Sub001_base "Control" 85 "Female" "White" 1350519.71
>>> Input Sub002_base "Control" 81.3  "Male" "White" 1558515.86
>>> Input Sub003_base "Control" 72.7  "Male" "White" 1187649.47
>>>
>>>
>>> Best,
>>> Zeng
>>>
>>>
>>>
>>> On Wed, Nov 10, 2021 at 6:38 PM Douglas N. Greve 
>>> wrote:
>>>
 Did you read the error message? It says:
 Variable 2 has character string Female
 Variables should be continuous numbers
 You have listed Gender and Race as strings, they have to be numbers
 (eg, 1, 2)
 You probably want to have these be discrete variables instead of
 continuous

 On 11/10/2021 6:20 PM, Zeng, Qi wrote:

 External Email - Use Caution
 Hi Douglas,

 Here is the command line:
 mri_glmfit \
   --y rh.thickness-rate.MyStudy.10.mgh \
   --fsgd FSGD/MyStudy.fsgd dods\
   --C Contrasts/Case-Control_age_gender_race_etiv.mtx\
   --surf fsaverage rh \
   --cortex \
   --glmdir rh.thickness-rate.MyStudy.10.mgh_age_gender_race_etiv.glmdir
 \
   --eres-save

 Also error message in terminal:
 gdfRead(): reading FSGD/MyStudy.fsgd
 WARNING: variable 1 is "Gender" which is often a discrete factor
   The proper way to handle discrete factors is to create classes.
   See *MailScanner has detected a possible fraud attempt from
 "secure-web.cisco.com" claiming to be*
 https://secure-web.cisco.com/1yZjSb88ByC6LpqTpxoDlPxIRkwZ4AgKf-ntdFS_UoHQnXxr47np6gUrWYww844iJ0PNYnyHPxIOTdlFT0LNYQ4JY3PiUg6T3L4kV1etuizRdwe_N71AadQjNvW3b0_zSQ4PzW9zJkM8pGuPHdxO3kx6Agto8vYpWfmr41hvWBH4evReluISnXKavQPG-VQAOkIisi_CblVa1hNsjrO3QZ8GaPH8ITQkNZTAkhzzvrmiMBfzcrZm67LElwLA_XyIz0ToXi2fSM9sBljnY2_RG2Xu-K4K5zxnCTCU-0iWlVWmekV-F57Et2wbEuchTKBii/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
 
 ERROR: gdfReadV1: Format Error: Input line 1, subjid = sub001_base
  Variable 2 has character string Female
>>

Re: [Freesurfer] question regarding FSGD file for coding discrete regressors

[Douglas N. Greve]

For DODS you would add 16 zeros (8 classes times 2 continuous variables)

On 11/11/2021 4:00 PM, Zeng, Qi wrote:


External Email - Use Caution

So for the DODS case, is "1 -1 1 -1 1 -1 1 -1 0 0 0 0" for the 
following FSGD:


GroupDescriptorFile 1
Title MyStudy
Class CaseMaleWhite
Class ControlMaleWhite
Class CaseMaleNonWhite
Class ControlMaleNonWhite
Class CaseFemaleWhite
Class ControlFemaleWhite
Class CaseFemaleNonWhite
Class ControlFemaleNonWhite
Variables age_bleTIV
InputSub001_baseControlFemaleWhite851350519.71
InputSub002_baseControlFemaleWhite81.31558515.86

Best,
Qi

On Thu, Nov 11, 2021 at 3:28 PM Douglas N. Greve 
 wrote:


For the DOSS case, yes.

On 11/11/2021 3:23 PM, Zeng, Qi wrote:


External Email - Use Caution

Hi  Douglas,

If to set up the FSGD as below, is my design matrix for case and
control comparison as "1 -1 1 -1 1 -1 1 -1 0 0"  ?

GroupDescriptorFile 1
Title MyStudy
Class CaseMaleWhite
Class ControlMaleWhite
Class CaseMaleNonWhite
Class ControlMaleNonWhite
Class CaseFemaleWhite
Class ControlFemaleWhite
Class CaseFemaleNonWhite
Class ControlFemaleNonWhite
Variables    AgeeTIV
InputSub001_base Control   Female  White   85     1350519.71
InputSub002_base Control   Female  White   81.3   1558515.86

Best,
Qi

On Thu, Nov 11, 2021 at 3:06 PM Douglas N. Greve
 wrote:

I would advice setting up the FSGD files with 8 classes based
on your 3 discrete, 2-level variables, eg, MaleControlWhite
then use two continuous variables Age and eTIV.
You should definitely normalize the eTIV (and probably age too)

On 11/10/2021 7:07 PM, Zeng, Qi wrote:


External Email - Use Caution

Hi Douglas,

Just to be clear, should I recode discrete variables as
numeric as sample1) or change discrete variables into
strings 2) or even change the comparison groups into strings
too 3)?
1)
Variables AgeGenderRaceeTIV
InputSub001_baseControl85111350519.71
InputSub002_baseControl81.3  011558515.86
InputSub003_baseControl81.3   001558515.86

or 2)
Variables AgeGenderRaceeTIV
InputSub001_baseControl85"Female""White"1350519.71
InputSub002_baseControl81.3 "Male""White"1558515.86
InputSub003_baseControl72.7 "Male""White"1187649.47

or 3)
Variables AgeGenderRaceeTIV
InputSub001_base"Control"85"Female""White"1350519.71
InputSub002_base"Control"81.3 "Male""White"1558515.86
InputSub003_base"Control"72.7 "Male""White"1187649.47


Best,
Zeng



On Wed, Nov 10, 2021 at 6:38 PM Douglas N. Greve
 wrote:

Did you read the error message? It says:
Variable 2 has character string Female
Variables should be continuous numbers
You have listed Gender and Race as strings, they have to
be numbers (eg, 1, 2)
You probably want to have these be discrete variables
instead of continuous

On 11/10/2021 6:20 PM, Zeng, Qi wrote:


External Email - Use Caution

Hi Douglas,

Here is the command line:
mri_glmfit \
  --y rh.thickness-rate.MyStudy.10.mgh \
  --fsgd FSGD/MyStudy.fsgd dods\
  --C Contrasts/Case-Control_age_gender_race_etiv.mtx\
  --surf fsaverage rh \
  --cortex \
  --glmdir
rh.thickness-rate.MyStudy.10.mgh_age_gender_race_etiv.glmdir
\
  --eres-save

Also error message in terminal:
gdfRead(): reading FSGD/MyStudy.fsgd
WARNING: variable 1 is "Gender" which is often a
discrete factor
  The proper way to handle discrete factors is to
create classes.
  See *MailScanner has detected a possible fraud
attempt from "secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples


ERROR: gdfReadV1: Format Error: Input line 1, subjid =
sub001_base
 Variable 2 has character string Female
 Variables should be continuous numbers
FSGDF Format Error: file = FSGD/MyStudy.fsgd, tag=Input

Also attached FSGD file below.
Thank you so much for the help!

Best,
Zeng




On Wed, N

Re: [Freesurfer] permutation simulation errror

[Douglas N. Greve]

What are the contents of 
/home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled? Can you send me the ls 
of it?


On 11/11/2021 3:38 PM, Brown, Alexander wrote:


External Email - Use Caution

Hi,

Now attached is the mri_glmfit-sim terminal output. the only output is 
the error message.


Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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


*Sent:* Thursday, November 11, 2021 2:27 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] permutation simulation errror
That is for mri_glmfit, not mri_glmfit-sim.

On 11/11/2021 3:24 PM, Brown, Alexander wrote:


External Email - Use Caution

Yes, please see the attached text file.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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

*Sent:* Thursday, November 11, 2021 2:04 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 

*Subject:* Re: [Freesurfer] permutation simulation errror
Can you capture and send the full terminal output from mri_glmfit-sim?

On 11/10/2021 10:41 PM, Brown, Alexander wrote:


External Email - Use Caution

Hi Dr. Greve,

I am using FS 6.0 on Ubuntu 18.04.

Unfortunately, no mri_glmfit-sim log file is generated when I 
attempt to run mri_glmfit-sim.


Best,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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

*Sent:* Wednesday, November 10, 2021 4:40 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 

*Subject:* Re: [Freesurfer] permutation simulation errror
WARNING: This message has originated from an External Source. This 
may be a phishing expedition that can result in unauthorized access 
to our IT System. Please use proper judgment and caution when 
opening attachments, clicking links, or responding to this email.
Which version of FS are you using? Can you send the log file created 
by mri_glmfit-sim (different than the one you sent)?


On 11/10/2021 3:49 PM, Brown, Alexander wrote:


External Email - Use Caution

Hello,

I am attempting to run a permutation simulation to correct for 
multiple comparisons and am getting the following error:


< mri_glmfit-sim --glmdir 
/home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled --perm 1000 1.3 
neg --perm-resid
ERROR: cannot find residual 
/home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres needed with 
--perm-resid

  when running mri_glmfit, make sure to include --eres-save >

Attached is the mri glmfit log. I ran the command with the 
--eres-save flag, and the eres.mgh file is generated in the glm 
directory.


I have downloaded the patch and have run this style of analysis 
multiple times without issue until today.


I appreciate any help!

Please let me know if you need any additional information.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

___
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] question regarding FSGD file for coding discrete regressors

[Zeng, Qi]

External Email - Use Caution

So for the DODS case, is "1 -1 1 -1 1 -1 1 -1 0 0 0 0" for the following
FSGD:

GroupDescriptorFile 1
Title MyStudy
Class CaseMaleWhite
Class ControlMaleWhite
Class CaseMaleNonWhite
Class ControlMaleNonWhite
Class CaseFemaleWhite
Class ControlFemaleWhite
Class CaseFemaleNonWhite
Class ControlFemaleNonWhite
Variables age_bl eTIV
Input Sub001_base ControlFemaleWhite 85 1350519.71
Input Sub002_base ControlFemaleWhite 81.3 1558515.86

Best,
Qi

On Thu, Nov 11, 2021 at 3:28 PM Douglas N. Greve 
wrote:

> For the DOSS case, yes.
>
> On 11/11/2021 3:23 PM, Zeng, Qi wrote:
>
> External Email - Use Caution
> Hi  Douglas,
>
> If to set up the FSGD as below, is my design matrix for case and control
> comparison as "1 -1 1 -1 1 -1 1 -1 0 0"  ?
>
> GroupDescriptorFile 1
> Title MyStudy
> Class CaseMaleWhite
> Class ControlMaleWhite
> Class CaseMaleNonWhite
> Class ControlMaleNonWhite
> Class CaseFemaleWhite
> Class ControlFemaleWhite
> Class CaseFemaleNonWhite
> Class ControlFemaleNonWhite
> VariablesAge eTIV
> Input Sub001_base  Control   Female  White   85 1350519.71
> Input Sub002_base  Control   Female  White   81.3   1558515.86
>
> Best,
> Qi
>
> On Thu, Nov 11, 2021 at 3:06 PM Douglas N. Greve 
> wrote:
>
>> I would advice setting up the FSGD files with 8 classes based on your 3
>> discrete, 2-level variables, eg, MaleControlWhite then use two continuous
>> variables Age and eTIV.
>> You should definitely normalize the eTIV (and probably age too)
>>
>> On 11/10/2021 7:07 PM, Zeng, Qi wrote:
>>
>> External Email - Use Caution
>> Hi Douglas,
>>
>> Just to be clear, should I recode discrete variables as numeric as
>> sample1) or change discrete variables into strings 2) or even change the
>> comparison groups into strings too 3)?
>> 1)
>> Variables Age Gender Race eTIV
>> Input Sub001_base Control 85 1 1 1350519.71
>> Input Sub002_base Control 81.3   0 1 1558515.86
>> Input Sub003_base Control 81.3   0 0 1558515.86
>>
>> or 2)
>> Variables Age Gender Race eTIV
>> Input Sub001_base Control 85 "Female" "White" 1350519.71
>> Input Sub002_base Control 81.3  "Male" "White" 1558515.86
>> Input Sub003_base Control 72.7  "Male" "White" 1187649.47
>>
>> or 3)
>> Variables  Age Gender Race eTIV
>> Input Sub001_base "Control" 85 "Female" "White" 1350519.71
>> Input Sub002_base "Control" 81.3  "Male" "White" 1558515.86
>> Input Sub003_base "Control" 72.7  "Male" "White" 1187649.47
>>
>>
>> Best,
>> Zeng
>>
>>
>>
>> On Wed, Nov 10, 2021 at 6:38 PM Douglas N. Greve 
>> wrote:
>>
>>> Did you read the error message? It says:
>>> Variable 2 has character string Female
>>> Variables should be continuous numbers
>>> You have listed Gender and Race as strings, they have to be numbers (eg,
>>> 1, 2)
>>> You probably want to have these be discrete variables instead of
>>> continuous
>>>
>>> On 11/10/2021 6:20 PM, Zeng, Qi wrote:
>>>
>>> External Email - Use Caution
>>> Hi Douglas,
>>>
>>> Here is the command line:
>>> mri_glmfit \
>>>   --y rh.thickness-rate.MyStudy.10.mgh \
>>>   --fsgd FSGD/MyStudy.fsgd dods\
>>>   --C Contrasts/Case-Control_age_gender_race_etiv.mtx\
>>>   --surf fsaverage rh \
>>>   --cortex \
>>>   --glmdir rh.thickness-rate.MyStudy.10.mgh_age_gender_race_etiv.glmdir \
>>>   --eres-save
>>>
>>> Also error message in terminal:
>>> gdfRead(): reading FSGD/MyStudy.fsgd
>>> WARNING: variable 1 is "Gender" which is often a discrete factor
>>>   The proper way to handle discrete factors is to create classes.
>>>   See *MailScanner has detected a possible fraud attempt from
>>> "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/1YCu4DNGxoLi5zalwi9XfWKMLYA4OOBRYPZEzRdP4RJSWFg4O4d3dLnnPVas8EHBUxfF4nSV-eC7ZFjIN1sY2rJwXO6iZ4xxPfGVfmY32_enNyymSd3OE8kX7WuqFkJwiPWLJf_BqmMMblUXJq5g8qaoRcoLASZyTMIRk13_MSQzmFbs1aA9JiImnKzvAUs6x74pkeHZFb9HR8i-1t7qcTREdnjKp7auywSjuJlcwgX31jHP0UBL2NTjFB5ExlTb8pXoNrXjeK7kegis1cJKEHt-qnLP2MROMOUN6pRnNwXi4MXcheqatZ6jHhynNPW-G/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
>>> 
>>> ERROR: gdfReadV1: Format Error: Input line 1, subjid = sub001_base
>>>  Variable 2 has character string Female
>>>  Variables should be continuous numbers
>>> FSGDF Format Error: file = FSGD/MyStudy.fsgd, tag=Input
>>>
>>> Also attached FSGD file below.
>>> Thank you so much for the help!
>>>
>>> Best,
>>> Zeng
>>>
>>>
>>>
>>>
>>> On Wed, Nov 10, 2021 at 5:41 PM Douglas N. Greve 
>>> wrote:
>>>
 please send your command line and full terminal output as well as the
 fsgd file

 On 11/10/2021

Re: [Freesurfer] permutation simulation errror

[Brown, Alexander]

External Email - Use Caution

Hi,

Now attached is the mri_glmfit-sim terminal output. the only output is the 
error message.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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

Sent: Thursday, November 11, 2021 2:27 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] permutation simulation errror

That is for mri_glmfit, not mri_glmfit-sim.

On 11/11/2021 3:24 PM, Brown, Alexander wrote:

External Email - Use Caution

Yes, please see the attached text file.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Thursday, November 11, 2021 2:04 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] permutation simulation errror

Can you capture and send the full terminal output from mri_glmfit-sim?

On 11/10/2021 10:41 PM, Brown, Alexander wrote:

External Email - Use Caution

Hi Dr. Greve,

I am using FS 6.0 on Ubuntu 18.04.

Unfortunately, no mri_glmfit-sim log file is generated when I attempt to run 
mri_glmfit-sim.

Best,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Wednesday, November 10, 2021 4:40 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] permutation simulation errror

WARNING: This message has originated from an External Source. This may be a 
phishing expedition that can result in unauthorized access to our IT System. 
Please use proper judgment and caution when opening attachments, clicking 
links, or responding to this email.
Which version of FS are you using? Can you send the log file created by 
mri_glmfit-sim (different than the one you sent)?

On 11/10/2021 3:49 PM, Brown, Alexander wrote:

External Email - Use Caution

Hello,

I am attempting to run a permutation simulation to correct for multiple 
comparisons and am getting the following error:

< mri_glmfit-sim --glmdir /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled 
--perm 1000 1.3 neg --perm-resid
ERROR: cannot find residual 
/home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres needed with --perm-resid
  when running mri_glmfit, make sure to include --eres-save >

Attached is the mri glmfit log. I ran the command with the --eres-save flag, 
and the eres.mgh file is generated in the glm directory.

I have downloaded the patch and have run this style of analysis multiple times 
without issue until today.

I appreciate any help!

Please let me know if you need any additional information.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/15F_9N6MApuS-SFvNjo0UgLU3b4lSfA4L5F1OTn7n8mfnIs9atqw3JevgrhlLsbv-_EuB_N82c5y-D8kCfzoQT_kSQ4aLSiOrXCtveFAS4LC-HMp5t0gNk7GP2M9RWCEJPxWlzvzCvsQZX4VwWD8a3oESyUh0p1GxldZaI0brAIrLnOoJpdgF9raBOgUo9TSt1ENqsoLGOTg5yqNk0iSoEZzXgVcP9LqquVuaVR6ZQB8h2aiY7SdKmAd5XBrw8nhiYJPUpm_NNU9_tAgeMLaMG5Ycw34ngd5U3ORvpUiL_ykxZbbR0T9cmZ5wEeKUa8ouQghuPaXfN5h9QXtP0b2rBQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

Re: [Freesurfer] permutation simulation errror

[Douglas N. Greve]

That is for mri_glmfit, not mri_glmfit-sim.

On 11/11/2021 3:24 PM, Brown, Alexander wrote:


External Email - Use Caution

Yes, please see the attached text file.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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


*Sent:* Thursday, November 11, 2021 2:04 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] permutation simulation errror
Can you capture and send the full terminal output from mri_glmfit-sim?

On 11/10/2021 10:41 PM, Brown, Alexander wrote:


External Email - Use Caution

Hi Dr. Greve,

I am using FS 6.0 on Ubuntu 18.04.

Unfortunately, no mri_glmfit-sim log file is generated when I attempt 
to run mri_glmfit-sim.


Best,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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

*Sent:* Wednesday, November 10, 2021 4:40 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
 
 

*Subject:* Re: [Freesurfer] permutation simulation errror
WARNING: This message has originated from an External Source. This 
may be a phishing expedition that can result in unauthorized access 
to our IT System. Please use proper judgment and caution when opening 
attachments, clicking links, or responding to this email.
Which version of FS are you using? Can you send the log file created 
by mri_glmfit-sim (different than the one you sent)?


On 11/10/2021 3:49 PM, Brown, Alexander wrote:


External Email - Use Caution

Hello,

I am attempting to run a permutation simulation to correct for 
multiple comparisons and am getting the following error:


< mri_glmfit-sim --glmdir 
/home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled --perm 1000 1.3 neg 
--perm-resid
ERROR: cannot find residual 
/home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres needed with 
--perm-resid

  when running mri_glmfit, make sure to include --eres-save >

Attached is the mri glmfit log. I ran the command with the 
--eres-save flag, and the eres.mgh file is generated in the glm 
directory.


I have downloaded the patch and have run this style of analysis 
multiple times without issue until today.


I appreciate any help!

Please let me know if you need any additional information.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

___
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] question regarding FSGD file for coding discrete regressors

[Douglas N. Greve]

For the DOSS case, yes.

On 11/11/2021 3:23 PM, Zeng, Qi wrote:


External Email - Use Caution

Hi  Douglas,

If to set up the FSGD as below, is my design matrix for case and 
control comparison as "1 -1 1 -1 1 -1 1 -1 0 0"  ?


GroupDescriptorFile 1
Title MyStudy
Class CaseMaleWhite
Class ControlMaleWhite
Class CaseMaleNonWhite
Class ControlMaleNonWhite
Class CaseFemaleWhite
Class ControlFemaleWhite
Class CaseFemaleNonWhite
Class ControlFemaleNonWhite
Variables    AgeeTIV
InputSub001_base Control   Female  White   85     1350519.71
InputSub002_base Control   Female  White   81.3   1558515.86

Best,
Qi

On Thu, Nov 11, 2021 at 3:06 PM Douglas N. Greve 
 wrote:


I would advice setting up the FSGD files with 8 classes based on
your 3 discrete, 2-level variables, eg, MaleControlWhite then use
two continuous variables Age and eTIV.
You should definitely normalize the eTIV (and probably age too)

On 11/10/2021 7:07 PM, Zeng, Qi wrote:


External Email - Use Caution

Hi Douglas,

Just to be clear, should I recode discrete variables as numeric
as sample1) or change discrete variables into strings 2) or even
change the comparison groups into strings too 3)?
1)
Variables AgeGenderRaceeTIV
InputSub001_baseControl85111350519.71
InputSub002_baseControl81.3  011558515.86
InputSub003_baseControl81.3   001558515.86

or 2)
Variables AgeGenderRaceeTIV
InputSub001_baseControl85"Female""White"1350519.71
InputSub002_baseControl81.3 "Male""White"1558515.86
InputSub003_baseControl72.7 "Male""White"1187649.47

or 3)
Variables AgeGenderRaceeTIV
InputSub001_base"Control"85"Female""White"1350519.71
InputSub002_base"Control"81.3 "Male""White"1558515.86
InputSub003_base"Control"72.7 "Male""White"1187649.47


Best,
Zeng



On Wed, Nov 10, 2021 at 6:38 PM Douglas N. Greve
 wrote:

Did you read the error message? It says:
Variable 2 has character string Female
Variables should be continuous numbers
You have listed Gender and Race as strings, they have to be
numbers (eg, 1, 2)
You probably want to have these be discrete variables instead
of continuous

On 11/10/2021 6:20 PM, Zeng, Qi wrote:


External Email - Use Caution

Hi Douglas,

Here is the command line:
mri_glmfit \
  --y rh.thickness-rate.MyStudy.10.mgh \
  --fsgd FSGD/MyStudy.fsgd dods\
  --C Contrasts/Case-Control_age_gender_race_etiv.mtx\
  --surf fsaverage rh \
  --cortex \
  --glmdir
rh.thickness-rate.MyStudy.10.mgh_age_gender_race_etiv.glmdir \
  --eres-save

Also error message in terminal:
gdfRead(): reading FSGD/MyStudy.fsgd
WARNING: variable 1 is "Gender" which is often a discrete factor
  The proper way to handle discrete factors is to create
classes.
  See *MailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples


ERROR: gdfReadV1: Format Error: Input line 1, subjid =
sub001_base
 Variable 2 has character string Female
 Variables should be continuous numbers
FSGDF Format Error: file = FSGD/MyStudy.fsgd, tag=Input

Also attached FSGD file below.
Thank you so much for the help!

Best,
Zeng




On Wed, Nov 10, 2021 at 5:41 PM Douglas N. Greve
 wrote:

please send your command line and full terminal output
as well as the fsgd file

On 11/10/2021 5:12 PM, Zeng, Qi wrote:


External Email - Use Caution

Hi Freesurfer experts,

Here, I want to design a simple group comparison (two
levels: Case vs. Control) and also count for 4
covariates (two continuous and two categoricals).
However, the GLM model cannot recognize my discrete
variables. What do you suggest to change?
>> FSDG file:
GroupDescriptorFile 1
Title MyStudy
Class Control
Class Case
Variables agegenderrace eTIV
Inputsub001_baseControl85FemaleWhite1350519
Contrast:
>> Design matrix for Case-Control and regress out the
effect of age, gender, race, and eTIV.
-1 1 0 0 0 0 0 0 0 0

Best,
Ze

Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats

[Douglas N. Greve]

I looked at your data. The problem is that the T2-pial placement is not 
very good.  In some places it is much thinner, in some places it it 
somewhat thicker. This makes the volume computation a little 
unpredictable (can't just assume that average thickenss*area will give  
you a reasonable value). The T2-pial is not placed well because the T2 
is very low resolution (3mm slice thickness); it is hard to determine 
the boundaries of a 2-3mm structure when your slices are 3mm



On 11/10/2021 10:55 AM, Castro Leal, Gonzalo wrote:


External Email - Use Caution

I have tried, but I get the following error:

local: Gonzalo_ADNI_sub-020S0899_T2.tar.gz remote: 
Gonzalo_ADNI_sub-020S0899_T2.tar.gz

421 Service not available, remote server has closed connection



*De:* freesurfer-boun...@nmr.mgh.harvard.edu 
 en nombre de Douglas N. Greve 


*Enviado:* miércoles, 10 de noviembre de 2021 15:09
*Para:* freesurfer@nmr.mgh.harvard.edu 
*Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
Ah, I see. Can you upload those two subjects using the method below?

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.


On 11/10/2021 9:33 AM, Castro Leal, Gonzalo wrote:


External Email - Use Caution

Sorry I did not explain myself well. For some regions of the brain 
this is what happens:


Region                    Num Vertices   Surf Area    GrayVol  ThickAvg
lateralorbitofrontal                     2969   2085   5489  2.469
lateralorbitofrontal                     2969   2085   5173  2.566
The first one corresponds to T1 only and the second one to T1 plus T2 
processing. The surface measurement is the same (this happens for all 
regions) however the volume decreases while the thickness increases, 
which is why I am confused.


PD: the last mail was sent by mistake, sorry for the spam.

Many thanks,
Gonzalo.

*De:* freesurfer-boun...@nmr.mgh.harvard.edu 
 
 
 en nombre de Douglas 
N. Greve  

*Enviado:* martes, 9 de noviembre de 2021 20:13
*Para:* freesurfer@nmr.mgh.harvard.edu 
 
 

*Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
In your first post, you said that you were confused as to why the 
thickness and volume were changing but the surface was not changing. 
Then you said that the pial surface changed. Does that answer your 
first question?


On 11/9/2021 1:33 PM, Castro Leal, Gonzalo wrote:


External Email - Use Caution

The time of the aparc.stats is 1h and 20min after the modification 
of the file pial.T2, and in the case of the T1 only processing the 
time stamp on the apar.stats is 20 min after the modification of the 
pial.T1. Does this answer your question or should I look into 
something else?


*De:* freesurfer-boun...@nmr.mgh.harvard.edu 
 
 
 en nombre de Douglas 
N. Greve  

*Enviado:* martes, 9 de noviembre de 2021 18:09
*Para:* freesurfer@nmr.mgh.harvard.edu 
 
 

*Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats
Were the stats files regenerated? Check the modification date

On 11/9/2021 10:41 AM, Castro Leal, Gonzalo wrote:


External Email - Use Caution

Yes the pial surface changed and the white did not.

*De:* freesurfer-boun...@nmr.mgh.harvard.edu 
 
 
 en nombre de 
Douglas N. Greve  


*Enviado:* martes, 9 de noviembre de 2021 14:49
*Para:* freesurfer@nmr.mgh.harvard.edu 
 
 


*Asunto:* Re: [Freesurfer] T1 aparc.stats vs T1 with T2 aparc.stats

⚠ Caution: External sender


The white surface won't change, but the pial surface should change. 
Can you verify that the pial surface changed?


On 11/9/2021 9:36 AM, Castro Leal, Gonzalo wrote:


External Email - Use Caution

Hello,

I wanted to compare the results of the aparc.stats on the same 
subjects when only the 

Re: [Freesurfer] permutation simulation errror

[Brown, Alexander]

External Email - Use Caution

Yes, please see the attached text file.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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

Sent: Thursday, November 11, 2021 2:04 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] permutation simulation errror

Can you capture and send the full terminal output from mri_glmfit-sim?

On 11/10/2021 10:41 PM, Brown, Alexander wrote:

External Email - Use Caution

Hi Dr. Greve,

I am using FS 6.0 on Ubuntu 18.04.

Unfortunately, no mri_glmfit-sim log file is generated when I attempt to run 
mri_glmfit-sim.

Best,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Wednesday, November 10, 2021 4:40 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] permutation simulation errror

WARNING: This message has originated from an External Source. This may be a 
phishing expedition that can result in unauthorized access to our IT System. 
Please use proper judgment and caution when opening attachments, clicking 
links, or responding to this email.
Which version of FS are you using? Can you send the log file created by 
mri_glmfit-sim (different than the one you sent)?

On 11/10/2021 3:49 PM, Brown, Alexander wrote:

External Email - Use Caution

Hello,

I am attempting to run a permutation simulation to correct for multiple 
comparisons and am getting the following error:

< mri_glmfit-sim --glmdir /home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled 
--perm 1000 1.3 neg --perm-resid
ERROR: cannot find residual 
/home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres needed with --perm-resid
  when running mri_glmfit, make sure to include --eres-save >

Attached is the mri glmfit log. I ran the command with the --eres-save flag, 
and the eres.mgh file is generated in the glm directory.

I have downloaded the patch and have run this style of analysis multiple times 
without issue until today.

I appreciate any help!

Please let me know if you need any additional information.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1nDMZ6K3qAiMIrZPax8x-66V_OKcT7eHjKejODXPTw3Aq5qN_uXVoE0ssm2CT8rahp04J__v1TmTGIl7BZXPSwUQtCTmLe8uGCBKLs9Ebr91IbnstPtoi5Tj2zk-AYqAg_LjLyd5lUXW4NQMXmpmnZ3lOEvstv5C6uGwlqrxzUL7oK468oAuK6cnfYw40pbcjW4MFb5nNRnw9pVf1Xubes0LwiM9AOVWzpbAY3wj4JuJo0FSuFxatCfhqlzaH1p2-MZeYioRnAogv1As82WWrXhsVvwzQWilpjAAc9wT4uB9cLJ6NgeYLfYNn-Kv5i1YLVWMajliO2G99RRcj3PbHcw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

Re: [Freesurfer] question regarding FSGD file for coding discrete regressors

[Zeng, Qi]

External Email - Use Caution

Hi  Douglas,

If to set up the FSGD as below, is my design matrix for case and control
comparison as "1 -1 1 -1 1 -1 1 -1 0 0"  ?

GroupDescriptorFile 1
Title MyStudy
Class CaseMaleWhite
Class ControlMaleWhite
Class CaseMaleNonWhite
Class ControlMaleNonWhite
Class CaseFemaleWhite
Class ControlFemaleWhite
Class CaseFemaleNonWhite
Class ControlFemaleNonWhite
VariablesAge eTIV
Input Sub001_base  Control   Female  White   85 1350519.71
Input Sub002_base  Control   Female  White   81.3   1558515.86

Best,
Qi

On Thu, Nov 11, 2021 at 3:06 PM Douglas N. Greve 
wrote:

> I would advice setting up the FSGD files with 8 classes based on your 3
> discrete, 2-level variables, eg, MaleControlWhite then use two continuous
> variables Age and eTIV.
> You should definitely normalize the eTIV (and probably age too)
>
> On 11/10/2021 7:07 PM, Zeng, Qi wrote:
>
> External Email - Use Caution
> Hi Douglas,
>
> Just to be clear, should I recode discrete variables as numeric as
> sample1) or change discrete variables into strings 2) or even change the
> comparison groups into strings too 3)?
> 1)
> Variables Age Gender Race eTIV
> Input Sub001_base Control 85 1 1 1350519.71
> Input Sub002_base Control 81.3   0 1 1558515.86
> Input Sub003_base Control 81.3   0 0 1558515.86
>
> or 2)
> Variables Age Gender Race eTIV
> Input Sub001_base Control 85 "Female" "White" 1350519.71
> Input Sub002_base Control 81.3  "Male" "White" 1558515.86
> Input Sub003_base Control 72.7  "Male" "White" 1187649.47
>
> or 3)
> Variables  Age Gender Race eTIV
> Input Sub001_base "Control" 85 "Female" "White" 1350519.71
> Input Sub002_base "Control" 81.3  "Male" "White" 1558515.86
> Input Sub003_base "Control" 72.7  "Male" "White" 1187649.47
>
>
> Best,
> Zeng
>
>
>
> On Wed, Nov 10, 2021 at 6:38 PM Douglas N. Greve 
> wrote:
>
>> Did you read the error message? It says:
>> Variable 2 has character string Female
>> Variables should be continuous numbers
>> You have listed Gender and Race as strings, they have to be numbers (eg,
>> 1, 2)
>> You probably want to have these be discrete variables instead of
>> continuous
>>
>> On 11/10/2021 6:20 PM, Zeng, Qi wrote:
>>
>> External Email - Use Caution
>> Hi Douglas,
>>
>> Here is the command line:
>> mri_glmfit \
>>   --y rh.thickness-rate.MyStudy.10.mgh \
>>   --fsgd FSGD/MyStudy.fsgd dods\
>>   --C Contrasts/Case-Control_age_gender_race_etiv.mtx\
>>   --surf fsaverage rh \
>>   --cortex \
>>   --glmdir rh.thickness-rate.MyStudy.10.mgh_age_gender_race_etiv.glmdir \
>>   --eres-save
>>
>> Also error message in terminal:
>> gdfRead(): reading FSGD/MyStudy.fsgd
>> WARNING: variable 1 is "Gender" which is often a discrete factor
>>   The proper way to handle discrete factors is to create classes.
>>   See *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1NEzix1p8cerzV2CscGJeOM5AxEOJi5zLORLiOeZ2wx-E6_vkK5NJqo-ry86kD_ktTitKimPz89haZ5YiKI_4QFVeWpS_2FVRxv4v08GpB0KFONvbcMNu8gXJXWC1jH0EgCJB7TExvThbl-TrnJRXNC9DL6fkI1EjUkdxMF1vblej9_5Js9YfDFO0Sm0_Dm7riTKQRk1rWAukdd7DQPVqsESboEgslbaclvRlzo-WERzaRjKLPE7OLHKD32WuHtT_tN0UAKlbTKFCXPm_ensblo6QhQDJnafIGxdB_3EqzyQZls7VQX1kP6qEE6XoXXIHmltlroSNZgmBMQofEYUMkg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsgdExamples
>> 
>> ERROR: gdfReadV1: Format Error: Input line 1, subjid = sub001_base
>>  Variable 2 has character string Female
>>  Variables should be continuous numbers
>> FSGDF Format Error: file = FSGD/MyStudy.fsgd, tag=Input
>>
>> Also attached FSGD file below.
>> Thank you so much for the help!
>>
>> Best,
>> Zeng
>>
>>
>>
>>
>> On Wed, Nov 10, 2021 at 5:41 PM Douglas N. Greve 
>> wrote:
>>
>>> please send your command line and full terminal output as well as the
>>> fsgd file
>>>
>>> On 11/10/2021 5:12 PM, Zeng, Qi wrote:
>>>
>>> External Email - Use Caution
>>> Hi Freesurfer experts,
>>>
>>> Here, I want to design a simple group comparison (two levels: Case vs.
>>> Control) and also count for 4 covariates (two continuous and two
>>> categoricals). However, the GLM model cannot recognize my discrete
>>> variables. What do you suggest to change?
>>> >> FSDG file:
>>> GroupDescriptorFile 1
>>> Title MyStudy
>>> Class Control
>>> Class Case
>>> Variables age gender race  eTIV
>>> Input sub001_base Control 85 Female White 1350519
>>> Contrast:
>>> >> Design matrix for Case-Control and regress out the effect of age,
>>> gender, race, and eTIV.
>>> -1 1 0 0 0 0 0 0 0 0
>>>
>>> Best,
>>> Zeng
>>>
>>>
>>>
>>>
>

Re: [Freesurfer] turning a surface label into 3d object

[Trisanna Sprung-Much]

External Email - Use Caution

thanks Doug - I will give this a try! Appreciate it.

--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute

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

Sent: Thursday, November 11, 2021 4:00 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] turning a surface label into 3d object

You can create a "patch" with something like
label2patch -surf white  fsaverage lh  lh.V1_exvivo.label ./lh.patch
then load it with
tksurferfv fsaverage lh white -patch ./lh.patch
When you load a patch, you will only be able to see the patch of the surface 
that you loaded it on
If you want to be able to toggle the whole surface on and off you can add -f 
fsaverage/surf/lh.white to the command line
It would be nice to be able to do this on-the-fly in freeview... someday



On 11/11/2021 10:33 AM, Trisanna Sprung-Much wrote:

External Email - Use Caution

Hi there

I realize this may be a bit of a stretch, but I wonder if there is any way to 
turn a surface label into its own 3D object that can then be examined on its 
own (to observe morphology) in Freeview? Similar to, for example, the sulcal 
skeletons that can be extracted in BrainVisa?

Many thanks~
Trisanna

--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1Aah6gjadjqTWuNcvPIB5YVtCPMBzcZS6iFfSpaXbNA26ogBiKdkkQ0ftBLPtXBfWBMzzyrNd_0EkYrnZOeHza4TLEWlSd92gu8B4qlqudn6n4nDgL59n9uso0jocdBPk_3AwreHsUDuNR94GZ029ySelVaHvAT0KaORGClKDfnUfNSXPUFs_yFw4_te84UWjNKnZWEgQRV9hgAex1u_iVx7FgwOdK3__e8IBvO-GlF8lrfOM4wG4CUWCtM_xo0c5KuCXk_NFpCHGDMkULllwnNMVGHfag3DENcYH61ykSl0orm87UM-5ptTIfzzBy7xD/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer

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

Re: [Freesurfer] question regarding FSGD file for coding discrete regressors

[Douglas N. Greve]

I would advice setting up the FSGD files with 8 classes based on your 3 
discrete, 2-level variables, eg, MaleControlWhite then use two 
continuous variables Age and eTIV.

You should definitely normalize the eTIV (and probably age too)

On 11/10/2021 7:07 PM, Zeng, Qi wrote:


External Email - Use Caution

Hi Douglas,

Just to be clear, should I recode discrete variables as numeric as 
sample1) or change discrete variables into strings 2) or even change 
the comparison groups into strings too 3)?

1)
Variables AgeGenderRaceeTIV
InputSub001_baseControl85111350519.71
InputSub002_baseControl81.3  011558515.86
InputSub003_baseControl81.3   001558515.86

or 2)
Variables AgeGenderRaceeTIV
InputSub001_baseControl85"Female""White"1350519.71
InputSub002_baseControl81.3 "Male""White"1558515.86
InputSub003_baseControl72.7 "Male""White"1187649.47

or 3)
Variables AgeGenderRaceeTIV
InputSub001_base"Control"85"Female""White"1350519.71
InputSub002_base"Control"81.3 "Male""White"1558515.86
InputSub003_base"Control"72.7 "Male""White"1187649.47


Best,
Zeng



On Wed, Nov 10, 2021 at 6:38 PM Douglas N. Greve 
 wrote:


Did you read the error message? It says:
Variable 2 has character string Female
Variables should be continuous numbers
You have listed Gender and Race as strings, they have to be
numbers (eg, 1, 2)
You probably want to have these be discrete variables instead of
continuous

On 11/10/2021 6:20 PM, Zeng, Qi wrote:


External Email - Use Caution

Hi Douglas,

Here is the command line:
mri_glmfit \
  --y rh.thickness-rate.MyStudy.10.mgh \
  --fsgd FSGD/MyStudy.fsgd dods\
  --C Contrasts/Case-Control_age_gender_race_etiv.mtx\
  --surf fsaverage rh \
  --cortex \
  --glmdir
rh.thickness-rate.MyStudy.10.mgh_age_gender_race_etiv.glmdir \
  --eres-save

Also error message in terminal:
gdfRead(): reading FSGD/MyStudy.fsgd
WARNING: variable 1 is "Gender" which is often a discrete factor
  The proper way to handle discrete factors is to create classes.
  See *MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples


ERROR: gdfReadV1: Format Error: Input line 1, subjid = sub001_base
 Variable 2 has character string Female
 Variables should be continuous numbers
FSGDF Format Error: file = FSGD/MyStudy.fsgd, tag=Input

Also attached FSGD file below.
Thank you so much for the help!

Best,
Zeng




On Wed, Nov 10, 2021 at 5:41 PM Douglas N. Greve
 wrote:

please send your command line and full terminal output as
well as the fsgd file

On 11/10/2021 5:12 PM, Zeng, Qi wrote:


External Email - Use Caution

Hi Freesurfer experts,

Here, I want to design a simple group comparison (two
levels: Case vs. Control) and also count for 4
covariates (two continuous and two categoricals). However,
the GLM model cannot recognize my discrete variables. What
do you suggest to change?
>> FSDG file:
GroupDescriptorFile 1
Title MyStudy
Class Control
Class Case
Variables agegenderrace eTIV
Inputsub001_baseControl85FemaleWhite1350519
Contrast:
>> Design matrix for Case-Control and regress out the effect
of age, gender, race, and eTIV.
-1 1 0 0 0 0 0 0 0 0

Best,
Zeng




___
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  



___
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/freesurf

Re: [Freesurfer] permutation simulation errror

[Douglas N. Greve]

Can you capture and send the full terminal output from mri_glmfit-sim?

On 11/10/2021 10:41 PM, Brown, Alexander wrote:


External Email - Use Caution

Hi Dr. Greve,

I am using FS 6.0 on Ubuntu 18.04.

Unfortunately, no mri_glmfit-sim log file is generated when I attempt 
to run mri_glmfit-sim.


Best,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

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


*Sent:* Wednesday, November 10, 2021 4:40 PM
*To:* freesurfer@nmr.mgh.harvard.edu 
*Subject:* Re: [Freesurfer] permutation simulation errror
WARNING: This message has originated from an External Source. This may 
be a phishing expedition that can result in unauthorized access to our 
IT System. Please use proper judgment and caution when opening 
attachments, clicking links, or responding to this email.
Which version of FS are you using? Can you send the log file created 
by mri_glmfit-sim (different than the one you sent)?


On 11/10/2021 3:49 PM, Brown, Alexander wrote:


External Email - Use Caution

Hello,

I am attempting to run a permutation simulation to correct for 
multiple comparisons and am getting the following error:


< mri_glmfit-sim --glmdir 
/home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled --perm 1000 1.3 neg 
--perm-resid
ERROR: cannot find residual 
/home/cns_2/Desktop/SC_PF_analysis/qdec/Untitled/eres needed with 
--perm-resid

  when running mri_glmfit, make sure to include --eres-save >

Attached is the mri glmfit log. I ran the command with the 
--eres-save flag, and the eres.mgh file is generated in the glm 
directory.


I have downloaded the patch and have run this style of analysis 
multiple times without issue until today.


I appreciate any help!

Please let me know if you need any additional information.

Thanks,
Alex

Alex Brown
CNS Core Facility
Department of Psychological Sciences
115 Melvin H. Marx Building
1416 Carrie Francke Drive
Columbia, MO 65211
Contact: 573-884-8779

___
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  



___
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
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 http://www.massgeneralbrigham.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.
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] [Re]:FsFastFunctionalConnectivityWalkthrough

[Douglas N. Greve]

sorry, can you include the previous emails in this thread along with 
your new questions?


On 11/11/2021 11:44 AM, Alice Giubergia wrote:


External Email - Use Caution

Thanks for your replies Doug!

1) Thanks.
2) Regarding question number 2, yes that was what I meant.
3) I ran the task analysis and extracted time series from unwhitened 
residuals by mri_segstats, upon a specific segmentation. I was 
thinking now of a correlation matrix by Pearson's coeff. Any further 
suggestions?


Also, I've got a pheraps silly question:
- When running a task analysis, I could specify -taskreg and -nuisreg 
separetly. My assumption is that only -nuisreg are regressed out from 
the data and that the residuals saved got task-related bold signal. Is 
it correct?
- If so, could I use task regressors as -nuisreg to get a "pseudo" 
resting state?


Hoping all question are clear,
Thanks for your patience,
Alice



___
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
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 http://www.massgeneralbrigham.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.
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] "No such file or directory" in wm

[Douglas N. Greve]

You cannot use flair as the main input. It has to be t1w; you can only 
use flair as an additional input to help fix the pial surface


On 11/11/2021 2:30 PM, Devarajan, Alex wrote:


External Email - Use Caution

Hello,

I'm running a fairly large database of MRIs through freesurfer for a 
project and have come into a number of errors - though I'm learning 
how to fix many of them, there are a few major categories of errors 
which are still difficult to parse out.


This was a sagittal T1 FLAIR sequence that I ran which produced the 
error "no such file or directory" when trying to access wm. I know 
that sometimes processing errors can lead to segmentation dumps, etc., 
but I'm unsure of where to proceed in fixing this and any help 
would be appreciated immensely.


I've attached a recon-all log as an example of this error for 
reference. Thank you!


___
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
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 http://www.massgeneralbrigham.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.
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] turning a surface label into 3d object

[Douglas N. Greve]

You can create a "patch" with something like
label2patch -surf white  fsaverage lh  lh.V1_exvivo.label ./lh.patch
then load it with
tksurferfv fsaverage lh white -patch ./lh.patch
When you load a patch, you will only be able to see the patch of the 
surface that you loaded it on
If you want to be able to toggle the whole surface on and off you can 
add -f fsaverage/surf/lh.white to the command line

It would be nice to be able to do this on-the-fly in freeview... someday



On 11/11/2021 10:33 AM, Trisanna Sprung-Much wrote:


External Email - Use Caution

Hi there

I realize this may be a bit of a stretch, but I wonder if there is any 
way to turn a surface label into its own 3D object that can then be 
examined on its own (to observe morphology) in Freeview? Similar to, 
for example, the sulcal skeletons that can be extracted in BrainVisa?


Many thanks~
Trisanna

--

/Trisanna Sprung-Much, PhD/
/Research Associate/
/McGill University
/
/Montreal Neurological Institute/

___
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
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 http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] [Re]:FsFastFunctionalConnectivityWalkthrough

[Alice Giubergia]

External Email - Use Caution

Thanks for your replies Doug!

1) Thanks.
2) Regarding question number 2, yes that was what I meant.
3) I ran the task analysis and extracted time series from unwhitened
residuals by mri_segstats, upon a specific segmentation. I was thinking now
of a correlation matrix by Pearson's coeff. Any further suggestions?

Also, I've got a pheraps silly question:
- When running a task analysis, I could specify -taskreg and -nuisreg
separetly. My assumption is that only -nuisreg are regressed out from the
data and that the residuals saved got task-related bold signal. Is it
correct?
- If so, could I use task regressors as -nuisreg to get a "pseudo" resting
state?

Hoping all question are clear,
Thanks for your patience,
Alice
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] turning a surface label into 3d object

[Trisanna Sprung-Much]

External Email - Use Caution

Hi there

I realize this may be a bit of a stretch, but I wonder if there is any way to 
turn a surface label into its own 3D object that can then be examined on its 
own (to observe morphology) in Freeview? Similar to, for example, the sulcal 
skeletons that can be extracted in BrainVisa?

Many thanks~
Trisanna

--

Trisanna Sprung-Much, PhD
Research Associate
McGill University
Montreal Neurological Institute
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer