[Freesurfer] Freesurfer VM password

[Zixuan Lin]

External Email - Use Caution

Hello!

I just downloaded the FS_7_2_0_ubuntu_18_04_06.ova.7z and would like to see if 
I can get the password to unzip this VM?

Thanks a lot,
Zixuan.
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Re: [Freesurfer] How to project SPM image

[Fischl, Bruce]

I see, and what's wrong with the screen shot you have? (and "Bruce" is fine).

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rachel Wagner
Sent: Sunday, July 3, 2022 7:41 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Hi Dr. Fischl,

My apologies, I don't have much of a background in software generally!

For the SPM image, I used the AAL atlas to label lesioned brain regions and 
colored by frequency to generate the heatmap. Image dimensions: 1x1x1, Image 
Size [91 109 91], Pixel Dimensions [2 2 2], Bits Per Pixel: 32. I will map onto 
fsaverage!

I'm hoping to display it as a heatmap on an average surface, to look something 
like this: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be | Decreased functional connectivity from 
Wernicke's area homologue in... | Download Scientific Diagram 
(researchgate.net)

This is a screenshot of what I currently have within FreeSurfer: MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be 
https://drive.google.com/file/d/150V0yIx6T1oSiCwiFmFiKU9rbNk1BfhD/view?usp=sharing

Thank you very much again for your help!
Rachel


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>>
Sent: Sunday, July 3, 2022 6:37:42 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to project SPM image


Can you give us more details? How did you create the 
rReslice_Combined_roi_meanRD.nii? What resolution is it? And how are you trying 
to display it? On an average surface? Why are you mapping it to bert and not 
fsaverage?



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Rachel Wagner
Sent: Sunday, July 3, 2022 6:26 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to project SPM image



External Email - Use Caution

Hello Dr. Fischl, thank you for your reply, it is much appreciated.



I am trying to cortically project my spm lesion location/frequency map, 
according to instructions linked here: AnalyzingData/MNE_SPM2Freesurfer - Meg 
Wiki 
(cam.ac.uk)



I have used the following code: bbregister --mov 
rReslice_Combined_roi_meanRD.nii --bold \ --s bert \ --init-rr --lta 
register.lta



However, my results still look very grainy. Is there a better way to do this?



Thank you again,

Rachel Wagner









From: Fischl, Bruce
Sent: June 30, 2022 9:09 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] How to project SPM image



Can you summarize what you are trying to do? What kind of overlay are you 
trying to visualize and what exactly do you mean by a "3D image"?



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Rachel Wagner
Sent: Thursday, June 30, 2022 2:48 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to project SPM image



External Email - Use Caution

Thank you so much for your response - I'm a master's student and am really 
struggling - 

Re: [Freesurfer] How to project SPM image

[Rachel Wagner]

External Email - Use Caution

Hi Dr. Fischl,

My apologies, I don’t have much of a background in software generally!

For the SPM image, I used the AAL atlas to label lesioned brain regions and 
colored by frequency to generate the heatmap. Image dimensions: 1x1x1, Image 
Size [91 109 91], Pixel Dimensions [2 2 2], Bits Per Pixel: 32. I will map onto 
fsaverage!

I’m hoping to display it as a heatmap on an average surface, to look something 
like this: | Decreased functional connectivity from Wernicke's area homologue 
in... | Download Scientific Diagram 
(researchgate.net)

This is a screenshot of what I currently have within FreeSurfer: 
https://secure-web.cisco.com/117ePUqDOWTzA8pswn-Mibsr2qBEZIMKV-Yd9P886w1Gz_L53sraXddp6xh_K6otFd1qp6tl3kHUNUk5TqYrNzizCdMJEp5zKR4XRSMj-pTdv0Us9VNWBasmYcsRRwLCrbr56qNZWBqSCMo1n9uuDVn2jwX3TJvflVYJ5eFy_AeuSRsYP4IZpVfIgQa_M_jpxzqEUcOyymM_iHc8lqsaOMkCXyzUnvQHwgy4EzHxKFkCoCHHa5jVAf9Gnol0mf4Yr2C8MosmAo4UiuPBgk6J_IX3DQcx-3NEMfUZdj7TOzoVG7H3Nuaid0CL4spvphW5d5l6r4qJCNk1rNi9tIb_xxQ/https%3A%2F%2Fdrive.google.com%2Ffile%2Fd%2F150V0yIx6T1oSiCwiFmFiKU9rbNk1BfhD%2Fview%3Fusp%3Dsharing

Thank you very much again for your help!
Rachel


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fischl, Bruce 

Sent: Sunday, July 3, 2022 6:37:42 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to project SPM image


Can you give us more details? How did you create the 
rReslice_Combined_roi_meanRD.nii? What resolution is it? And how are you trying 
to display it? On an average surface? Why are you mapping it to bert and not 
fsaverage?



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rachel Wagner
Sent: Sunday, July 3, 2022 6:26 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to project SPM image



External Email - Use Caution

Hello Dr. Fischl, thank you for your reply, it is much appreciated.



I am trying to cortically project my spm lesion location/frequency map, 
according to instructions linked here: AnalyzingData/MNE_SPM2Freesurfer - Meg 
Wiki 
(cam.ac.uk)



I have used the following code: bbregister --mov 
rReslice_Combined_roi_meanRD.nii --bold \ --s bert \ --init-rr --lta 
register.lta



However, my results still look very grainy. Is there a better way to do this?



Thank you again,

Rachel Wagner









From: Fischl, Bruce
Sent: June 30, 2022 9:09 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] How to project SPM image



Can you summarize what you are trying to do? What kind of overlay are you 
trying to visualize and what exactly do you mean by a “3D image”?



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Rachel Wagner
Sent: Thursday, June 30, 2022 2:48 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to project SPM image



External Email - Use Caution

Thank you so much for your response – I’m a master’s student and am really 
struggling - I’ve been stuck trying to do this for about 2 weeks now, so the 
help is so appreciated!



My results look very grainy in mricron so my supervisor wants me to keep trying 
in FreeSurfer unfortunately for me.



I uploaded a the brain.mgz volume in freeview, but I’m not sure how to add an 
overlay and project as a 3D image. Would you happen to have any ideas?



Thank you so, so much again,

Rachel Wagner



From: niels.f...@gmx.de
Sent: June 30, 2022 2:35 PM
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] How to project SPM image



You don't often get email from niels.f...@gmx.de. 
Learn why this is 

Re: [Freesurfer] trac-all -prep -c ERROR

[Yendiki, Anastasia]

Is the brainstem cut off from the diffusion scan? A bit hard to tell from the 
pics but this could be the problem.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Salar Dini, Elaheh 

Sent: Thursday, June 30, 2022 7:58 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] trac-all -prep -c ERROR


External Email - Use Caution

Hi back,

Should be alright now. Please try this link: MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be 
https://drive.google.com/drive/folders/1pkss2G7AYmlrCWYPVItnctl4W7H_OV7W?usp=sharing

Thank you,
Ela



Yendiki, 
Anastasia
 Thu, 30 Jun 2022 14:18:47 
-0700

Hi Ela - Can you make the google doc accessible by all?

Anastasia.


From: Salar Dini, Elaheh 
Sent: Thursday, June 30, 2022 5:08 PM
To: Freesurfer support list 
Subject: Re: trac-all -prep -c ERROR


Thank you for the reply. For some reason, when I change the DCM file to nii and 
look at them, in majority of our subjects, the cerebellum and lower brain stem 
has been cut off, but in this specific subject, I don't think the CST is 
truncated or out of field more than any other subjects that the TRACULA steps 
have been run for without any errors. I have taken a few screenshots of both 
this subject and another one whom -prep and -bedp have been run for without any 
errors and uploaded them to google drive. Please find the link here:

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://drive.google.com/file/d/1twW57_d5f1G32GtcxYp-A2u2OsnQF3kF/view?usp=sharing

Moreover, it is worth mentioning that this specific subject had profound global 
atrophy with diagnosis of Alzheimer's.


As always, I appreciate your time and help.

Kind regards,

Ela






Yendiki, 
Anastasia
 Wed, 29 Jun 2022 08:41:26 
-0700

Any chance that part of the left CST is truncated in 

Re: [Freesurfer] How to project SPM image

[Fischl, Bruce]

Can you give us more details? How did you create the 
rReslice_Combined_roi_meanRD.nii? What resolution is it? And how are you trying 
to display it? On an average surface? Why are you mapping it to bert and not 
fsaverage?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rachel Wagner
Sent: Sunday, July 3, 2022 6:26 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Hello Dr. Fischl, thank you for your reply, it is much appreciated.

I am trying to cortically project my spm lesion location/frequency map, 
according to instructions linked here: AnalyzingData/MNE_SPM2Freesurfer - Meg 
Wiki 
(cam.ac.uk)

I have used the following code: bbregister --mov 
rReslice_Combined_roi_meanRD.nii --bold \ --s bert \ --init-rr --lta 
register.lta

However, my results still look very grainy. Is there a better way to do this?

Thank you again,
Rachel Wagner




From: Fischl, Bruce
Sent: June 30, 2022 9:09 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] How to project SPM image

Can you summarize what you are trying to do? What kind of overlay are you 
trying to visualize and what exactly do you mean by a "3D image"?

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Rachel Wagner
Sent: Thursday, June 30, 2022 2:48 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Thank you so much for your response - I'm a master's student and am really 
struggling - I've been stuck trying to do this for about 2 weeks now, so the 
help is so appreciated!

My results look very grainy in mricron so my supervisor wants me to keep trying 
in FreeSurfer unfortunately for me.

I uploaded a the brain.mgz volume in freeview, but I'm not sure how to add an 
overlay and project as a 3D image. Would you happen to have any ideas?

Thank you so, so much again,
Rachel Wagner

From: niels.f...@gmx.de
Sent: June 30, 2022 2:35 PM
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] How to project SPM image

You don't often get email from niels.f...@gmx.de. 
Learn why this is 
important
Sure is, through freeview, however if you already have spm format files, it is 
much easier to use mricron

Von: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 Im Auftrag von Rachel Wagner
Gesendet: Donnerstag, 30. Juni 2022 18:18
An: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Betreff: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Thanks very much, I will absolutely do so! Just so I know - is there not any 
way of generating such figures in Freesurfer?

From: niels.f...@gmx.de
Sent: June 30, 2022 4:47 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] How to project SPM image

You don't often get email from niels.f...@gmx.de. 
Learn why this is 
important

External Email - Use Caution
Rachel,  these figures were likely created with a software called mricron, not 
freesurfer.  Check it out :)

Holen Sie sich Outlook für 

Re: [Freesurfer] How to project SPM image

[Rachel Wagner]

External Email - Use Caution

Hello Dr. Fischl, thank you for your reply, it is much appreciated.

I am trying to cortically project my spm lesion location/frequency map, 
according to instructions linked here: AnalyzingData/MNE_SPM2Freesurfer - Meg 
Wiki 
(cam.ac.uk)

I have used the following code: bbregister --mov 
rReslice_Combined_roi_meanRD.nii --bold \ --s bert \ --init-rr --lta 
register.lta

However, my results still look very grainy. Is there a better way to do this?

Thank you again,
Rachel Wagner




From: Fischl, Bruce
Sent: June 30, 2022 9:09 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] How to project SPM image

Can you summarize what you are trying to do? What kind of overlay are you 
trying to visualize and what exactly do you mean by a “3D image”?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rachel Wagner
Sent: Thursday, June 30, 2022 2:48 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Thank you so much for your response – I’m a master’s student and am really 
struggling - I’ve been stuck trying to do this for about 2 weeks now, so the 
help is so appreciated!

My results look very grainy in mricron so my supervisor wants me to keep trying 
in FreeSurfer unfortunately for me.

I uploaded a the brain.mgz volume in freeview, but I’m not sure how to add an 
overlay and project as a 3D image. Would you happen to have any ideas?

Thank you so, so much again,
Rachel Wagner

From: niels.f...@gmx.de
Sent: June 30, 2022 2:35 PM
To: 'Freesurfer support list'
Subject: Re: [Freesurfer] How to project SPM image

You don't often get email from niels.f...@gmx.de. 
Learn why this is 
important
Sure is, through freeview, however if you already have spm format files, it is 
much easier to use mricron

Von: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 Im Auftrag von Rachel Wagner
Gesendet: Donnerstag, 30. Juni 2022 18:18
An: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Betreff: Re: [Freesurfer] How to project SPM image


External Email - Use Caution
Thanks very much, I will absolutely do so! Just so I know – is there not any 
way of generating such figures in Freesurfer?

From: niels.f...@gmx.de
Sent: June 30, 2022 4:47 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] How to project SPM image

You don't often get email from niels.f...@gmx.de. 
Learn why this is 
important

External Email - Use Caution
Rachel,  these figures were likely created with a software called mricron, not 
freesurfer.  Check it out :)

Holen Sie sich Outlook für 
Android



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Freesurfer mailing list
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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail 

Re: [Freesurfer] segmentation corpus callosum

[Fischl, Bruce]

Sure, just run your subject through recon-all, then use mri_binarize or 
mri_extract_label to pull the cc labels out of the aseg.

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Mostafa Fakhri
Sent: Sunday, July 3, 2022 1:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] segmentation corpus callosum


External Email - Use Caution
Hello to all,

I was wondering if I could create a binary mask of corpus callosum from T1w 
images in subject space with FS.


Thanks for the help!
Mostafa



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

[Mostafa Fakhri]

External Email - Use Caution

Hello to all,

I was wondering if I could create a binary mask of corpus callosum from T1w
images in subject space with FS.


Thanks for the help!
Mostafa
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

[Freesurfer] Pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z

[Sharma, Maya]

Hello,

I am downloading Freesurfer on my Windows device; may I please have the pass 
code to expand the archive FS_7_2_0_Ubuntu_18_04_06.ova.7z

Thank you kindly

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