Re: [Freesurfer] Freeview does not display image

2022-10-03 Thread fsbuild 
External Email - Use Caution

Hello Justina,
We need to know what your setup is on Windows for running Linux in order to 
help with running freeview.  It reads like you are not using VirtualBox to 
run the Linux Ubuntu OS,
 I do not have VirtualBox installed ...
So it’s not clear to me how you are currently running Ubuntu Linux on your 
Windows machine in order to run freeview or other freesurfer commands. 
 Are you running Ubuntu linux with the Windows Subsystem for Linux (WSL)? 
 Maybe you are connecting remotely to a linux machine via VNC or the like 
from your Windows machine ? 

If you don’t mind running freesurfer 7.2.0 (instead of the newest 7.3.2 
release), there is a smaller version of the VM to download 
from https://secure-web.cisco.com/1YWO9PWAWb2dUg45HhJ8-Uf5BVRKini-Plt5R0ZzrEI56U73eIIqsvtOabP978uAZGbMguO6zYQXj2qmsPJoTTh7XQB1Lfjd_GAeMNqapxT92fvVsg3gtB6o_K_TGqYKm52s7ec5nvDnfb305SkZY5SoJ35m3yTBjgDCFLbXXPxXkheXpgZ_WR53HyCMzoKJTA3AY00j28VO95fGeTZ7uWfvDvLe8v_Og6PX24DOCLRBZTaLzr9cWE2lBsMd6N0avVNQetV_emJ79GF0lrvGJSxK2kaC87ydb09ZWR2FVyUPprRlBNZm7zdFvyF1pcMsa/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67%26nbsp;
 with setup instructions under that link.   But you would still need 
to download and install VirtualBox on your Windows machine and then download 
and install the Freesurfer Software.
- R.

On Oct 3, 2022, at 09:35, Justina Lee  
wrote:External Email - Use 
CautionTo whom that can provide 
any insight,I am currently using Ubuntu on windows to open freeview to show 
some data. My issue at hand is that freeview does not show any images, despite 
changing the window levels (contrast and brightness). Using the command 
freeview -v works, and I am able to run it smoothly. When I try to open an mgz 
file, it runs fine, but I am unable to see anything.  I do not have 
VirtualBox installed and tried to take this advice from previous but I ran 
across the problem of downloading the course Virtual Machine. I do think that I 
do not need to download the VirtualBox and can continue using Ubuntu on 
Windows.What could be the issue with this? Should I be downloading the Virtual 
machine to run Freeview?Thank you so much for your time and I hope that my 
issue is not too big of a problem to 
solve.Sincerely,Justina___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] Freeview does not display image

2022-10-03 Thread Justina Lee 
External Email - Use Caution

To whom that can provide any insight,

I am currently using Ubuntu on windows to open freeview to show some data.
My issue at hand is that freeview does not show any images, despite
changing the window levels (contrast and brightness). Using the command
freeview -v works, and I am able to run it smoothly. When I try to open an
mgz file, it runs fine, but I am unable to see anything.

 I do not have VirtualBox installed and tried to take this advice from
previous but I ran across the problem of downloading the course Virtual
Machine. I do think that I do not need to download the VirtualBox and can
continue using Ubuntu on Windows.

What could be the issue with this? Should I be downloading the Virtual
machine to run Freeview?

Thank you so much for your time and I hope that my issue is not too big of
a problem to solve.

Sincerely,
Justina
___
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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 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

2022-10-03 Thread fernanda rohrsetzer 
External Email - Use Caution

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



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

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

Re: [Freesurfer] mri_glmfit error

2022-10-03 Thread 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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