Re: [Freesurfer] Command not found

[Huang, Yujing]

External Email - Use Caution

Hi Rachel,

Have you sourced Freesurfer install directory?

Here is help page on how to setup your Freesurfer environment on Linux - 
https://secure-web.cisco.com/1Ub7K0QLalONiy0rW3bBM14kqwMElWC9S8wklOMGTNEoROLtbi5l-vQB0xjZDlZmXEwIz_EwWsnjfnVZZ7ljJGZLQ9u9dqRcNnHcLBEzuN0plpPm9cbi8s1TXEmiyDt_2tmnVdIzkMVk2q0_tbwTP9yZjp0Q27SkOoNU0gWBvaPIZdFM4rKjFadBaGbel6vVYBKQkPmgrIwYQCK1ThtThkJVQxakYhqa4PuElpuRgI9YWpReeD22AXkApfi7p0BAswT_GSXQa0yUcgQqNFbkeVw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FSetupConfiguration_Linux

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rachel Wagner
Sent: Sunday, July 30, 2023 10:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Command not found


External Email - Use Caution

Hello all,

I have not used freesurfer in a couple of months, and have returned to create a 
new cortical projection image. I'm having an issue with my commands, they don't 
seem to be recognized anymore and I'm not sure why:

developer@developer-VirtualBox:~/freesurfer$ freeview

Command 'freeview' not found, did you mean:

  command 'treeview' from deb treeview

Try: sudo apt install 



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

Re: [Freesurfer] Freeview ERROR: label name '3rd-Ventricle' is duplicated (FSv6.0.0 with updated Freeview)

[Wang, Ruopeng]

External Email - Use Caution

Have you tried the latest Mac build of freeview? This has been fixed recently.

On Jul 30, 2023, at 11:02 AM, Ha Manh Luu 
mailto:hal4...@med.cornell.edu>> wrote:


External Email - Use Caution



From: Ha Manh Luu
Sent: Thursday, July 20, 2023 10:38 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freeview ERROR: label name '3rd-Ventricle' is duplicated

Hello FreeSurfer Developers,

This is a follow up email.

I have installed FreeSurfer v6.0.0 in my MacOS 12.6.7 but I got Freeview 
crashed due to PETSC error (which has been fixed in FreeSurfer v7.1.1).

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/12bN_GdNSv2Ik7XN85oA3_ALo3usTg2uRRXhq5huLnfPJALe1wLKA90W0nYTXQzBkMMMwXkhalWdkNKtttdZX4VO3IoecjP2n6ZQWnSsBJ-6pm3IHgDJfJYL58MYAFgT3LsHo-h56WBWKPtYjLnw_wekGT0Qv4-jLor4uRE63YStSaxcmR3FtakpVstY5GyYhdTdzuH7uP9hKMgcognzvGVhOIRxWlcyOAAAhnqWsSZbJukpw8dUY4rsYc0VYbiGqQyZwhV2ayV7SEmRzn5BQ_w/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel6downloads

For the consistency with my previous work, I do not want to upgrade to 
Freesurfer V7.x in my MAC.

I updated freeview from this website:
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://secure-web.cisco.com/1R1MsBHl0X1wmxG2J-0IPMwdJZBuAorLiw5witdVKJsjxWOZiITWTedjvVSJZKn77jLGiK-KnLbqBu-HZty6oFViZgp3LXnDX123uG1tZV3BcVMfkdh7_uzrjaV1xre6RQ6UXMd7nNbS7A_ObSs5vG13dWPOvfBA6XiZaJQoIjqLPOCMwVxM6iV24-fmDg4BXkuv32160p54tWtG4O08qgz7apm7Xj4zxBXINk-NpVE8iI_cqKLvZmMJPOgwL1ER5Xj__AIbu4RPSypij-LBwHw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FUpdateFreeview

After updating the Freeview, it works for me but it still shows the following 
error:
ERROR: label name '3rd-Ventricle' is duplicated! ERROR: label name 
'3rd-Ventricle' is duplicated! CTABfindDuplicateNames: 1 duplicate names found 
in: 
/private/var/folders/4w/c9v2n39j3hd_4rb1bmyrftqwgt/T/FreeSurferColorLUT.txt

I cat the file and see that '3rd-Ventricle' has 2 lablels in the file. I also 
see that the FreeSurferColorLUT.txt file is not identical to the 
FreeSurferColorLUT.txt in FreeSurfer home folder.

Can you tell me what is the file FreeSurferColorLUT.txt for and the issue is 
serious or not? If so, how to fix this?

  1.  Freesurfer version:  freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0

2)  Platform: MacOS Darwin 12.6.7

  1.  freeview:  ERROR: label name '3rd-Ventricle' is duplicated! ERROR: label 
name '3rd-Ventricle' is duplicated! CTABfindDuplicateNames: 1 duplicate names 
found in: 
/private/var/folders/4w/c9v2n39j3hd_4rb1bmyrftqwgt/T/FreeSurferColorLUT.txt
  2.  FreeSurferColorLUT.txt: see attached

Thanks,

Ha
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1FuF1OcSpvNEYqS-07bu_TvVIT_YPDU8jFR3d0VBJZvWpbtQYd_5FZfSkFco6LZumfVIheE5UoJD4oOrXKIafKAEXQX650D4tISq-vnZP_YibnJ8GMZMlvKD0oQcxfyxZWluLNgUmbPuxiwMAXZmFiAHsscX8RZTyFHqbLtdJ7mrAUkQ9hi_75iYhPcDX7zoaWqWpCDc8QpI-pafhGYOunlmYrKLEIhRQyxAyCfA52LsYwMavO8k8xcAUnluW49oEBnmcKl9ZQpdQ-xrW-CP9oA/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
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 co

Re: [Freesurfer] mri_watershed and improvements of skullstripping

[Huang, Yujing]

External Email - Use Caution

Hi Michelangelo,

I'm wondering if you are using FS 7.3.2?   'DOCAREG' was accidentally dropped 
for autonrecon2. You can fix it by adding '-careg' at the end of command line.

Best,

Yujing


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Michelangelo Fabbrizzi
Sent: Sunday, July 30, 2023 11:34 AM
To: freesurfer@nmr.mgh.harvard.edu; fsbuild ; 
freesurfer-ow...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_watershed and improvements of skullstripping


External Email - Use Caution
Dear All,

another question: after the below if I use the command to run autorecon2:
recon-all -s sub-01_recon -autorecon2

I get the following error:
ERROR: cannot find or read transforms/talairach.m3z

Can you help me please?

Thanks, regards,

Michelangelo


Il giorno 30 lug 2023, alle ore 15:32, Michelangelo Fabbrizzi 
mailto:michef...@gmail.com>> ha scritto:

Dear Freesurfer experts,

I am new to FS, and I would have couple of questions.
I used in sequence:
A- recon-all -i sub-01_T1w.nii.gz -s sub-01_recon -autorecon1
B- recon-all -skullstrip -wsthresh 5 -clean-bm -s sub-01_recon
C- recon-all -skullstrip -clean-bm -gcut -subjid sub-01_recon

The brainmask.mgz obtained is good (no skull, brain is okay), however if I now 
use mri_watershed to obtain the bem surfaces, it looks the brainmask.mgz is not 
used and it is created a new one called ws.mgz that still contain some piece of 
skull that generate wrong BEM surfaces; even using -h 5 the result is not 
optimal:
mri_watershed -h 5 -useSRAS -surf 
/Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/sub-01_recon 
/Users/michelangelo/Test_skullstripping/sub-01_recon/mri/T1.mgz 
/Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/ws.mgz

I am wondering:
- how can I force the mri_watershed command to use the brainmask.mgz already 
created after step C above, instead of creating a new one?
- is it possible to use the -gcut command also for mri_watershed?

Thanks, appreciated,

Miche


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

Re: [Freesurfer] mri_watershed and improvements of skullstripping

[Michelangelo Fabbrizzi]

External Email - Use CautionDear Yujing,yes, I am using FS 7.3.2, so thanks I will try withrecon-all -s sub-01_recon -autorecon2 -caregshould I add the -careg also for the -autorecon3 step?Can you eventually have a look also at the questions in my first email below (at the very bottom of this email trail)?Greatly appreciated!Il giorno 31 lug 2023, alle ore 14:51, Huang, Yujing  ha scritto:





External Email - Use Caution

Hi Michelangelo,
 
I’m wondering if you are using FS 7.3.2?   ‘DOCAREG’ was accidentally dropped for autonrecon2. You can fix it by adding ‘-careg’ at the end of command line.
 
Best,
 
Yujing
 
 


From: freesurfer-boun...@nmr.mgh.harvard.edu 
On Behalf Of Michelangelo Fabbrizzi
Sent: Sunday, July 30, 2023 11:34 AM
To: freesurfer@nmr.mgh.harvard.edu; fsbuild ; freesurfer-ow...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_watershed and improvements of skullstripping


 
External Email - Use Caution
Dear All,

 


another question: after the below if I use the command to run autorecon2:


recon-all -s sub-01_recon -autorecon2


 


I get the following error:



ERROR: cannot find or read transforms/talairach.m3z


 


Can you help me please?


 


Thanks, regards,


 


Michelangelo







Il giorno 30 lug 2023, alle ore 15:32, Michelangelo Fabbrizzi  ha scritto:

 


Dear Freesurfer experts,

I am new to FS, and I would have couple of questions.
I used in sequence:
A- recon-all -i sub-01_T1w.nii.gz -s sub-01_recon -autorecon1

B- recon-all -skullstrip -wsthresh 5 -clean-bm -s sub-01_recon

C- recon-all -skullstrip -clean-bm -gcut -subjid sub-01_recon

The brainmask.mgz obtained is good (no skull, brain is okay), however if I now use mri_watershed to obtain the bem surfaces, it looks the brainmask.mgz is not used and it is created a new one called ws.mgz that still contain some piece of skull that generate
 wrong BEM surfaces; even using -h 5 the result is not optimal:
mri_watershed -h 5 -useSRAS -surf /Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/sub-01_recon /Users/michelangelo/Test_skullstripping/sub-01_recon/mri/T1.mgz /Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/ws.mgz

I am wondering:
- how can I force the mri_watershed command to use the brainmask.mgz already created after step C above, instead of creating a new one?
- is it possible to use the -gcut command also for mri_watershed?

Thanks, appreciated,

Miche






 




___Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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  .___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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_watershed and improvements of skullstripping

[Huang, Yujing]

External Email - Use Caution

You don’t need ‘-careg’ if you just run autorecon3.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Michelangelo Fabbrizzi
Sent: Monday, July 31, 2023 8:55 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mri_watershed and improvements of skullstripping


External Email - Use Caution
Dear Yujing,

yes, I am using FS 7.3.2, so thanks I will try with

recon-all -s sub-01_recon -autorecon2 -careg

should I add the -careg also for the -autorecon3 step?

Can you eventually have a look also at the questions in my first email below 
(at the very bottom of this email trail)?

Greatly appreciated!


Il giorno 31 lug 2023, alle ore 14:51, Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>> ha scritto:


External Email - Use Caution
Hi Michelangelo,

I’m wondering if you are using FS 7.3.2?   ‘DOCAREG’ was accidentally dropped 
for autonrecon2. You can fix it by adding ‘-careg’ at the end of command line.

Best,

Yujing


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Michelangelo Fabbrizzi
Sent: Sunday, July 30, 2023 11:34 AM
To: freesurfer@nmr.mgh.harvard.edu; 
fsbuild mailto:fsbu...@contbay.com>>; 
freesurfer-ow...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_watershed and improvements of skullstripping


External Email - Use Caution
Dear All,

another question: after the below if I use the command to run autorecon2:
recon-all -s sub-01_recon -autorecon2

I get the following error:
ERROR: cannot find or read transforms/talairach.m3z

Can you help me please?

Thanks, regards,

Michelangelo



Il giorno 30 lug 2023, alle ore 15:32, Michelangelo Fabbrizzi 
mailto:michef...@gmail.com>> ha scritto:

Dear Freesurfer experts,

I am new to FS, and I would have couple of questions.
I used in sequence:
A- recon-all -i sub-01_T1w.nii.gz -s sub-01_recon -autorecon1
B- recon-all -skullstrip -wsthresh 5 -clean-bm -s sub-01_recon
C- recon-all -skullstrip -clean-bm -gcut -subjid sub-01_recon

The brainmask.mgz obtained is good (no skull, brain is okay), however if I now 
use mri_watershed to obtain the bem surfaces, it looks the brainmask.mgz is not 
used and it is created a new one called ws.mgz that still contain some piece of 
skull that generate wrong BEM surfaces; even using -h 5 the result is not 
optimal:
mri_watershed -h 5 -useSRAS -surf 
/Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/sub-01_recon 
/Users/michelangelo/Test_skullstripping/sub-01_recon/mri/T1.mgz 
/Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/ws.mgz

I am wondering:
- how can I force the mri_watershed command to use the brainmask.mgz already 
created after step C above, instead of creating a new one?
- is it possible to use the -gcut command also for mri_watershed?

Thanks, appreciated,

Miche



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1ifXI2CrT6fdUd0Izxj6gRSO4lqIKipD6XZ2lWVS5fWo-1XP9KVYGuiTyxskS7i3rjP7mw4VhZVHr8vIpg8aD2j2EqMxofJDgMAmpfInk0ZQepJ6QH0q8RVr3Zx2UrwIS9ix01tRuxOJcB6qr21GJIiMONrps6udNoU6z080K4cG8QsTEni290ZsBvPoJk9VdT8WnKolzwRNPAkA1CfucpmDPh20kaltTwwtDJncYoN5Rm2kL-z4P9Wzhr1B_tHkKvJznoemd-UUg9un46xgNtQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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://secure-web.cisco.com/1Vc9SOMD5QGa_ciVc0xydm7dUgGwJRUqQPnEQUMWTtlwYu7BtmejcKKr8T8w9casBoBMISqVb-FCj4KTlm1p9FxUHuEttFBWw1Lc_KLV8Z2gIt-L9iziV2fnFZwzH0B92rMyjF6HAgKPPlUYC4GfjF3u4Je2NoMa14x_Rd8VlgDXt87-2AdWH1ZJ4n6en3e5yYjrPYvUYIjmHA3QcqSJFCUanSfgEvzuhIHhZiM6k76hola68md_NsqZId41trdcJ_oiIxlMhPdMz-7zOlkSb4w/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
 

 .
___
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/compli

Re: [Freesurfer] mri_watershed and improvements of skullstripping

[Huang, Yujing]

External Email - Use Caution

I'm not sure how to force mri_watershed command to use the brainmask.mgz 
already created.

Recon-all '-gcut' is achieved by running mri_gcut after mri_watershed.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Michelangelo Fabbrizzi
Sent: Sunday, July 30, 2023 9:32 AM
To: freesurfer@nmr.mgh.harvard.edu; fsbuild ; 
freesurfer-ow...@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed and improvements of skullstripping

External Email - Use Caution

Dear Freesurfer experts,

I am new to FS, and I would have couple of questions.
I used in sequence:
A- recon-all -i sub-01_T1w.nii.gz -s sub-01_recon -autorecon1   
B- recon-all -skullstrip -wsthresh 5 -clean-bm -s sub-01_recon  
C- recon-all -skullstrip -clean-bm -gcut -subjid sub-01_recon

The brainmask.mgz obtained is good (no skull, brain is okay), however if I now 
use mri_watershed to obtain the bem surfaces, it looks the brainmask.mgz is not 
used and it is created a new one called ws.mgz that still contain some piece of 
skull that generate wrong BEM surfaces; even using -h 5 the result is not 
optimal:
mri_watershed -h 5 -useSRAS -surf 
/Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/sub-01_recon 
/Users/michelangelo/Test_skullstripping/sub-01_recon/mri/T1.mgz 
/Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/ws.mgz

I am wondering:
- how can I force the mri_watershed command to use the brainmask.mgz already 
created after step C above, instead of creating a new one?
- is it possible to use the -gcut command also for mri_watershed?

Thanks, appreciated,

Miche




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1cF5CFj8ObeEdVU_l8xNGBdbJJ0PpzQ0VrSp5AzRUYXgIxGRUfeyVxaZ9CYyltHFOjkFZr3L3v8Sj-Q43KuOROdbHN-BlQ3kEJGstPNrP89sh3tzlULMEJfhOIV7yDG5cLd7US9Kdx53lxH37tG4cbcrN_SIdEfVaeujvuwgCe_pY9kNgRR711jNjJ2Gju8uAvp6b5417gKL24XKNTz3S6v3aZhiUihlhwcdxG299RmBHNNN8FcuFLe-cD6e0ldB-GgQiuKLGfy6Wc1IOUQpuKw/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
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] (no subject)

[Nolan, Jackson]

External Email - Use Caution

Hello,

'timepoints' refers to the individual scan sessions that make up a longitudinal 
dataset for a subject.

i.e. If a subject was scanned 3 times, say in 2010, 2015, and 2020, this 
subject would have 3 timepoints. One from each year they were scanned.

Best,
Jackson

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Atwater, Emanuel R 

Sent: Thursday, July 27, 2023 6:15 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] (no subject)


External Email - Use Caution

Hello FreeSurfer Team,



I recently messaged about running a longitudinal scan on a couple of images.



The response told me to utilize “timepoints”:

For base processing, specify each timepoint with -tp <> (not the nii file).

recon-all -base  -tp  -tp  ... -all



I’ve attempted to review the youtube videos and instructions made available 
online but am unsure what “timepoints” are. Can I have some clarification on 
what exactly a timepoint is, please.



FS version: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b

Recon-all.log: see attached



V/r,

Emanuel Atwater


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

Re: [Freesurfer] mri_watershed and improvements of skullstripping

[Michelangelo Fabbrizzi]

External Email - Use Caution

Dear Yujing,

thanks again for your help, just a last question, how can give to autorecon1 
the input to use certain options at the mri_watershed step (for instance a 
certain preflood height (-h 5) or use of the atlas option (-atlas))?

recon-all -s sub-01_recon -i T1w.nii.gz -autorecon1 

Your help is greatly appreciated!

Michelangelo

> Il giorno 31 lug 2023, alle ore 17:23, Huang, Yujing 
>  ha scritto:
> External Email - Use Caution
> 
> I'm not sure how to force mri_watershed command to use the brainmask.mgz 
> already created.
> 
> Recon-all '-gcut' is achieved by running mri_gcut after mri_watershed.
> 
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  On Behalf Of Michelangelo Fabbrizzi
> Sent: Sunday, July 30, 2023 9:32 AM
> To: freesurfer@nmr.mgh.harvard.edu; fsbuild ; 
> freesurfer-ow...@nmr.mgh.harvard.edu
> Subject: [Freesurfer] mri_watershed and improvements of skullstripping
> 
>External Email - Use Caution
> 
> Dear Freesurfer experts,
> 
> I am new to FS, and I would have couple of questions.
> I used in sequence:
> A- recon-all -i sub-01_T1w.nii.gz -s sub-01_recon -autorecon1
> B- recon-all -skullstrip -wsthresh 5 -clean-bm -s sub-01_recon
> C- recon-all -skullstrip -clean-bm -gcut -subjid sub-01_recon
> 
> The brainmask.mgz obtained is good (no skull, brain is okay), however if I 
> now use mri_watershed to obtain the bem surfaces, it looks the brainmask.mgz 
> is not used and it is created a new one called ws.mgz that still contain some 
> piece of skull that generate wrong BEM surfaces; even using -h 5 the result 
> is not optimal:
> mri_watershed -h 5 -useSRAS -surf 
> /Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/sub-01_recon
>  /Users/michelangelo/Test_skullstripping/sub-01_recon/mri/T1.mgz 
> /Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/ws.mgz
> 
> I am wondering:
> - how can I force the mri_watershed command to use the brainmask.mgz already 
> created after step C above, instead of creating a new one?
> - is it possible to use the -gcut command also for mri_watershed?
> 
> Thanks, appreciated,
> 
> Miche
> 
> 
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1cF5CFj8ObeEdVU_l8xNGBdbJJ0PpzQ0VrSp5AzRUYXgIxGRUfeyVxaZ9CYyltHFOjkFZr3L3v8Sj-Q43KuOROdbHN-BlQ3kEJGstPNrP89sh3tzlULMEJfhOIV7yDG5cLd7US9Kdx53lxH37tG4cbcrN_SIdEfVaeujvuwgCe_pY9kNgRR711jNjJ2Gju8uAvp6b5417gKL24XKNTz3S6v3aZhiUihlhwcdxG299RmBHNNN8FcuFLe-cD6e0ldB-GgQiuKLGfy6Wc1IOUQpuKw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1cTHii2jK1prD_CnADwRM4fGIQbTqO7yHAtvDOSHvIUNYRGRbxoZMXfSSnHb33WRj4ejM84mowaRwVZIGGyJqCffQc13gzZrBbUUGiNSxMnsPaonRdhTOwLQ3GhEnjxTWH6EHJ3dEtgWtzTJ8TfcgSZVu9ka4oSJ5fleh_m5gi0LveysoML4KLApySqFDDOfdGx4JaHXemN9lCXDCMje-jp-_qskKNhXbY-yP-V_CvrOlx4E5V60bcJv7j063TumpulbZYMv0vxWR9Vcmg6w2GsNDCNMmQO1llRCYoTGhj3koFztD4iKLZRJQU4aG0qLQbPaSJWYdnZW-u7Wp9V2k9w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 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://secure-web.cisco.com/19ZF3Eo2hejHW73PfG4iB-XcRcs7fDWd8GwCtm3h9M_CC3_u6UtvHsVzHGJ-1ZaDUpHru1S1350N_ophruGMIVTSUAv64GW-Hwy_XyWmghNedfA49x6wRn00_gB0ImsWecfgk-dZV6zDjqYm-SO-bvmNVa-Ef1VWLS5LsKI0Jg_XBgMJ5b732gLMmCbhfEKJSepG9O0C8raL9wICrMzY89GNBrSv7dTYxKxxdLKCUIzdyircSGYJ8bI-SXqUeemRvcRtOTWchnl6BVYrtEQhzg_HfULERNoDWNcgo6IVkMQt-6628n4GLwL1ikksBbpWBzc_8Slb_7LKNXneCZrN6oA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  
> 
>  .
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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] Freesurfer version and Installation

[hmarz...@student.ubc.ca]

External Email - Use Caution

Dear Freesurfer developers,

Previously, I downloaded the 
freesurfer-linux-centos7_x86_64-dev-20230331-e304091 version and successfully 
analyzed some data using this version. Now, I find myself in the need to 
reinstall Freesurfer, but I am unable to locate the source file on your website.

Could you kindly guide me to where I can find the mentioned version? 
Alternatively, if this specific version is no longer available, please advise 
me on which version I should download and install to achieve the same results 
as before.

Thank you very much for your assistance.


Regards

Hengameh

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

[fsbuild]

External Email - Use Caution

Development builds are continually updated and may not be stable, i.e., so the 
March 31st development build is no longer available.  I suggest using one 
of the release builds listed on the release page.  The 7.4.1 build from 
this June is the most recent release there with download links.
- R.
https://secure-web.cisco.com/1mozD5gXusZi5ReWhcLJuHVCFslf2OLCNdFPx2ADAwbvA7IQmu6CJloyJy4WRglnOG5x3qTETxLYWCPrW6vkgqEATbhfcH6627JL1FOXgSuAsF6s79LQ750-fva-wrYBwqeaTA9U2Qmy6l7Wx0uzgcEYkg-v8-dlujR6qgtDg11NkOGtemOCc_1ZKpJxDbctw0qc8bn5oY0MxdJACP_mpcTwBWrIjxmOF68wNworwPDCxjUVueyKuQVH3fV_hQ3rZhrwF5WzUSgB8VvFAFTKcz8RSYrB6Q4-ycqgVvBa9JcICYePX4LpHG5Q9aw8FVDQ76L24Ng0pYhCeqV1Xh9rz8A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads

On Jul 31, 2023, at 14:38, hmarz...@student.ubc.ca 
wrote:External Email - Use 
CautionDear Freesurfer 
developers,Previously, I downloaded the 
freesurfer-linux-centos7_x86_64-dev-20230331-e304091 version and successfully 
analyzed some data using this version. Now, I find myself in the need to 
reinstall Freesurfer, but I am unable to locate the source file on your 
website.Could you kindly guide me to where I can find the mentioned version? 
Alternatively, if this specific version is no longer available, please advise 
me on which version I should download and install to achieve the same results 
as before.Thank you very much for your 
assistance.RegardsHengameh___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://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
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] Code not working

[Rachel Wagner]

External Email - Use Caution

Hello all,

I’m getting an error as follows:

developer@developer-VirtualBox:~/freesurfer$ setenv SUBJECTS_DIR 
$FREESURFER_HOME/subjects

Command 'setenv' not found, did you mean:

  command 'getenv' from snap getenv (0.3.1)

See 'snap info ' for additional versions.

developer@developer-VirtualBox:~/freesurfer$



Is something not installed? These functions were working previously.

Thanks,
Rachel
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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] Code not working

[fsbuild]

External Email - Use Caution

 It reads like you downloaded and setup the public VM 
(from https://secure-web.cisco.com/1YpN3buNDQ0c9lVvFb2LEMMoXu4bGzcQrSQ6ddm7xsasVOV9uJhcsnEgL1Hc1mSNTG6VXMshwnJdqirgu2VRs15W0S-so_lVY_Zs4BzyCsjkRnrwG9WvOGP2d5Ouk04JzWWWwFTI7BGpwgkV95xP86xw6PpMlHcWLUAikPSqZfhOoZNNRnbkZmLBShFNEjh4KBAV9Sp8XhoekmpjdpHmHKYbzYZ6rjfc3Rga_QqSJHypW-uNpSdDsYzsi_6ZekkcC9KOb1WRaNW-_T35cv1gDF2rhmoI7XQDUVTX3Wo4M2XuLsX242UOqpsRtQwyqEdYG/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67),
 and had it working ?
If so, as shown by the screenshot at the bottom of that web page, the 
freesurfer environment is already setup by default when a new terminal window 
opens (and in that screenshot is using bash but not csh/tcsh).  You should 
not have to be setting the environment variables by hand as they appear listed 
at the top of the screenshot of the terminal.
If your $HOME/.bashrc file was edited/changed, or you changed the default shell 
from bash to csh/tcsh, then it’s possible that setup is no longer working.
If you accepted one of the prompts to *upgrade* the system to a newer version 
of Ubuntu, then the setup may no longer be working.
For the public VM, this file should list you are running Ubuntu 18.04
$ cat /etc/os-release NAME="Ubuntu"VERSION="18.04.6 LTS (Bionic 
Beaver)"ID=ubuntuID_LIKE=debianPRETTY_NAME="Ubuntu 18.04.6 
LTS"VERSION_ID=“18.04”… rest of output deleted ...
If your system was upgraded it will probably say Ubuntu 20.
- R.
On Jul 31, 2023, at 16:31, Rachel Wagner  
wrote:External Email - Use 
CautionHello 
all,  I’m getting an error as 
follows: developer@developer-VirtualBox:~/freesurfer$
 setenv SUBJECTS_DIR $FREESURFER_HOME/subjects Command 'setenv' not found, 
did you mean:   command 'getenv' from snap getenv (0.3.1) See 
'snap info ' for additional 
versions. developer@developer-VirtualBox:~/freesurfer$   Is 
something not installed? These functions were working 
previously. Thanks, Rachel___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://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
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] infantFS download

[Katie Rose Jobson]

External Email - Use Caution

Hi FS experts,

I was just wondering about how long it takes to receive the download for 
infantFS. I would like to use the program to analyze my dissertation data, so I 
just want to have a timeframe in mind for about how long it will take to start 
to use it! I have already requested the code, so hopefully I am not missing 
anything.

Thanks so much for your help!

Best Wishes,
Katie


--
Katie Jobson, M.S. | Personal 
Website
Board Member | Coding Outreach 
Group
Ph.D. Student | Cognitive Neuroscience 
Lab
Department of Psychology and Neuroscience | Temple University

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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] MAC OS Ventura problems

[Alan Francis]

External Email - Use Caution

Hi Doug et al,

I recently moved from Linux to MAC OS running Ventura. When I run the
recon-all, it gives me this message:

“mri_compute_overlap” cannot be opened because the developer cannot be
verified.

The help given at the FS website is for previous MAC versions. Ventura does
not allow what is shown on the website.

Any suggestions?

Thanks,

Alan
-- 
*|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|*



*Alan N. Francis PhDAssistant Professor of NeuroscienceInstitute of
Neuroscience*
*University of Texas, School of Medicine*

*Rio Grande Valley*

*Texas.*
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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_watershed and improvements of skullstripping

[Douglas N. Greve]

   External Email - Use Caution

there are not options to autorecon1 specifically. You can pass some 
watershed args on the command line, but it is probably easier to use an 
expert options file, eg, create a text file (eg, xopts.txt) with 
something like

mri_watershed -less
then run recon-all with -expert xopts.txt (and the rest of your args)
You can add as many options as you want to that line

On 7/31/2023 1:22 PM, Michelangelo Fabbrizzi wrote:


External Email - Use Caution

Dear Yujing,

thanks again for your help, just a last question, how can give to 
autorecon1 the input to use certain options at the mri_watershed step 
(for instance a certain preflood height (-h 5) or use of the atlas 
option (-atlas))?


recon-all -s sub-01_recon -i T1w.nii.gz -autorecon1 

Your help is greatly appreciated!

Michelangelo

Il giorno 31 lug 2023, alle ore 17:23, Huang, Yujing 
 ha scritto:


   External Email - Use Caution

I'm not sure how to force mri_watershed command to use the 
brainmask.mgz already created.


Recon-all '-gcut' is achieved by running mri_gcut after mri_watershed.

-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Michelangelo 
Fabbrizzi

Sent: Sunday, July 30, 2023 9:32 AM
To: freesurfer@nmr.mgh.harvard.edu; fsbuild ; 
freesurfer-ow...@nmr.mgh.harvard.edu

Subject: [Freesurfer] mri_watershed and improvements of skullstripping

   External Email - Use Caution

Dear Freesurfer experts,

I am new to FS, and I would have couple of questions.
I used in sequence:
A- recon-all -i sub-01_T1w.nii.gz -s sub-01_recon -autorecon1
B- recon-all -skullstrip -wsthresh 5 -clean-bm -s sub-01_recon
C- recon-all -skullstrip -clean-bm -gcut -subjid sub-01_recon

The brainmask.mgz obtained is good (no skull, brain is okay), however 
if I now use mri_watershed to obtain the bem surfaces, it looks the 
brainmask.mgz is not used and it is created a new one called ws.mgz 
that still contain some piece of skull that generate wrong BEM 
surfaces; even using -h 5 the result is not optimal:
mri_watershed -h 5 -useSRAS -surf 
/Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/sub-01_recon 
/Users/michelangelo/Test_skullstripping/sub-01_recon/mri/T1.mgz 
/Users/michelangelo/Test_skullstripping/sub-01_recon/bem/watershed/ws.mgz


I am wondering:
- how can I force the mri_watershed command to use the brainmask.mgz 
already created after step C above, instead of creating a new one?

- is it possible to use the -gcut command also for mri_watershed?

Thanks, appreciated,

Miche




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1cF5CFj8ObeEdVU_l8xNGBdbJJ0PpzQ0VrSp5AzRUYXgIxGRUfeyVxaZ9CYyltHFOjkFZr3L3v8Sj-Q43KuOROdbHN-BlQ3kEJGstPNrP89sh3tzlULMEJfhOIV7yDG5cLd7US9Kdx53lxH37tG4cbcrN_SIdEfVaeujvuwgCe_pY9kNgRR711jNjJ2Gju8uAvp6b5417gKL24XKNTz3S6v3aZhiUihlhwcdxG299RmBHNNN8FcuFLe-cD6e0ldB-GgQiuKLGfy6Wc1IOUQpuKw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/15k8N-Zo4AKDYaXF49SR8hi6D1Ts33kcqH2-zVmVVMdx_wYSEpXxC-rSwtJiecx6qlFIVgt-51BJOM5LZsE_ljTF9wwpyXuoQ3wI-wmss1Z7NEk1k9V7Y2gOts_89x281g-1Fh0WLdVN7mXlzRSFr20A7N0R2BmRGbNX-tB5mQlz7HTEKagZoiun9I6gbpgn_Flj9imjx5uDE_3yqNiUikyZaiG9bE5hdaPAoYN87fqNiuiYAo7gEtm8XR2vvArrr/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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://secure-web.cisco.com/1lYbMeUuB3ZNZzX5_HF-RzuItvwTGVyuABaYThW437kw_lsdMuaS3KofGAQlE1PXtnzXXCqtHc1eMhJYz6zonGfAznIJFJ-fKcKrm-fDUDU7pv4yRCwGP0IsrxUyqHOvTBIRm3Wcp56rC5t9tBdF5M3s3ukjZjLCOWvP7z5asuohDd51LZCHZ9Pj6rl-BqvXSHZU4WwsvodG1Qgg3DXBrRo3c0yhlt4bBmLdaYHFEiRemaqKiMinIlO_1KTqSjt0f/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline 
 .




___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/15k8N-Zo4AKDYaXF49SR8hi6D1Ts33kcqH2-zVmVVMdx_wYSEpXxC-rSwtJiecx6qlFIVgt-51BJOM5LZsE_ljTF9wwpyXuoQ3wI-wmss1Z7NEk1k9V7Y2gOts_89x281g-1Fh0WLdVN7mXlzRSFr20A7N0R2BmRGbNX-tB5mQlz7HTEKagZoiun9I6gbpgn_Flj9imjx5uDE_3yqNiUikyZaiG9bE5hdaPAoYN87fqNiuiYAo7gEtm8XR2vvArrr/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
_

Re: [Freesurfer] Remove border vertices

[Douglas N. Greve]

   External Email - Use Caution


there is not an easy way to do it, but there is a way
1. convert the annot to labels using mri_annotation2label
2. for each label, run mri_label2label with the --erode option to create 
a new set of labels (different folder)

3. use mris_label2annot to recombine them into an annotation

On 7/26/2023 4:35 AM, Marina Fernández wrote:


External Email - Use Caution

Dear experts,

I would like to project a parcellation (annot file) onto the cortical 
surface removing or hiding the border vertices of the different labels 
of the parcellation. I thought that I can do that scripting but first 
I would need to know which vertices are border vertices. Or is there a 
simpler way to do it?


Thank you very much in advance.
Bets regards,
Marina

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1geVDxstW9zK2wotl_jKnHxotXVTBKQFqfSbkJyltlbQ12m1-NZNmESYZa2gqvSfmMavi2j79FVGnuT3HkXEEFcrttDBYQs1_plOaYK_uYzq_5nZHEeMuqQYf3Y9H3fafE2M-eTpHCx7nzU0HDGH1HUgr_hwmF6A_rB2qw7CNqEqR1mSOa02nfYqnjo35A4EnuIvCqmUoib6naKZo06yKEaYNEoI_ymBAQrArXEZxetajnUvjAJExK4tbAczevaXUqCPlhkkvwrIV-Cf42BmNLg/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
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Tkregister2 GUI not responding fully

[Douglas N. Greve]

   External Email - Use Caution


Try adding --no-surfs

On 7/24/2023 12:45 PM, Viktorija Pratuseviciute wrote:


External Email - Use Caution

Thank you very much! We did try the command tkregisterfv --s PI163 
–fstal, however the recon-all processing fails before a surf/lh.white 
file is created and therefore an error is produced that this file 
can’t be found. Seems like with tkregisterfv the default is for it to 
require the lh.white file?


Many thanks,

Viki

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


*Date: *Friday, July 21, 2023 at 6:28 AM
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Re: [Freesurfer] Tkregister2 GUI not responding fully

*External Email - Use Caution *

tkregister2 is pretty old at this point; try using tkregsiterfv with 
the same option.


On 7/20/2023 7:06 PM, Viktorija Pratuseviciute wrote:

*External Email - Use Caution *

Hello,

We are trying to process a scan with a failed talairach. We have
been able to visualize the misalignment and attempted to use the
following command (tkregister2 --s PI163 –fstal) to manual adjust
the talairach.xfm based on the tutorial
(FsTutorial/Talairach_freeview).

The tkregister2 GUI opens up, however only certain functions work:
I can switch between target and moveable, I can also double click
on sliding scales to switch coronal, saggital and horizontal
views, however I am not able to move any of the sliders including
the rotate or translate brain and hence unable to fix the
talairach. Is there a way to fix this issue? Or an alternative way
to fix the bad talairach output?

We are using freesurfer/7.3.1 and have attempted the command on
our server command line on both mac and windows with same results.

Many thanks,

Viki



___

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/120PqAOhYldrRrLIEevPVe3qHhq_ir5ey6gQy-1IlNTowbI6kI9RiR3mD-h-DQgD5KCvR_PuGkpvOMQJOQ0ilNIYSNyLHR_EW5t3PRaH21YVii0o_kF5ZLyW_u2WKpejG-2GuZzvgB5GvFxVuG2L5BxRtyf8nZV_90M3ADSCGGsDcTIzvaTKqRn3XO2YiZvGKIYNf72dck2TvjM7n146i8Eem2vkJg1LSaLiVHUwXR_e8pAo8lP59p0mH0VcrIOFG/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
  



___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/120PqAOhYldrRrLIEevPVe3qHhq_ir5ey6gQy-1IlNTowbI6kI9RiR3mD-h-DQgD5KCvR_PuGkpvOMQJOQ0ilNIYSNyLHR_EW5t3PRaH21YVii0o_kF5ZLyW_u2WKpejG-2GuZzvgB5GvFxVuG2L5BxRtyf8nZV_90M3ADSCGGsDcTIzvaTKqRn3XO2YiZvGKIYNf72dck2TvjM7n146i8Eem2vkJg1LSaLiVHUwXR_e8pAo8lP59p0mH0VcrIOFG/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
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] Unable to read in images from Freeview command window

[Rachel Wagner]

External Email - Use Caution

Hello,

I am looking to cortically project onto a pial surface and am trying to use the 
following code in the freeview GUI to do so:

[FreeView] -v 004/mri/wm.mgz:colormap=jet 004/mri/brainmask.mgz -f 
004/surf/lh.pial:edgecolor=blue 004/surf/lh.white:edgecolor=red
error: mghRead(/home/developer/freesurfer/004/mri/wm.mgz, -1): could not open 
file
MRIread failed: Unable to read from /home/developer/freesurfer/004/mri/wm.mgz


I don’t know how to resolve this, any guidance would be greatly appreciated.

Thank you,
Rachel Wagner
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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] Unable to read in images from Freeview command window

[Douglas N. Greve]

   External Email - Use Caution


does 004/mri/wm.mgz exist?

On 7/31/2023 6:40 PM, Rachel Wagner wrote:


External Email - Use Caution

Hello,

I am looking to cortically project onto a pial surface and am trying 
to use the following code in the freeview GUI to do so:


[FreeView] -v 004/mri/wm.mgz:colormap=jet 004/mri/brainmask.mgz -f 
004/surf/lh.pial:edgecolor=blue 004/surf/lh.white:edgecolor=red


error: mghRead(/home/developer/freesurfer/004/mri/wm.mgz, -1): could 
not open file


MRIread failed: Unable to read from 
/home/developer/freesurfer/004/mri/wm.mgz


I don’t know how to resolve this, any guidance would be greatly 
appreciated.


Thank you,

Rachel Wagner


___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1pDLX1alA2mVCJ2Fju5AmNd8ADxbS8GO421gwhKbmX9-ptfVO3mwOHbm_gCOLpkuzRBYGvTonkxPuNEfTpY7HURcvP5araoBMUj05STYdd_XtStjwZ6r7EGaRNbcvoLWF4QR9vCKo9-ZFzTUeAR-4oph73PjutTO6xXURhmphJHDi_FRj6QkoO26SL2I3ZsyRdirbzXbiuPSseMwI87-IL6Qw-nCETA_nxjDqVT762DVE6VVapCRIXXK1YsJttT6S/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
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] MAC OS Ventura problems

[fsbuild]

External Email - Use Caution

 Try right clicking on the .pkg installer and select “open with” and then 
select “installer.app”.  That should allow you to do an install of the 
distribution which will go under /Applications/freesurfer/7.4.1, e.g., for the 
7.4.1 release pkg obtained via the link,  
https://secure-web.cisco.com/1Ykhf9FuCkslH36IMqiGn4EMsGDCmsjO4PjpHzy0g-46r2qdha91TANU8SFDrimatGl58ckmpzSIKFLBBEDeE-rThr46c4ePHZYZH-3NJscnR1JHGMSbUZhJMZGOPMVnBKBHd_G5shtHfKxOah-qDeGcY_oYO8i6QaE_D4nMTzJk_3dSGf_xgQBmqlkw1VLWdkpAfqFzmINaw8umUhwqdynOZRuTk61_H4tKyyrFijOREAsKZzrtzytdY3WLwzq_YPx8ASmCEFdirs7-LanT6Dmj004LCGy-377GgbIo5KaKngeIA3T2qxm7aIQj6Hy_UxJ-TymwpxSDAjIuQGbHtug/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer-macOS-darwin_x86_64-7.4.1.pkg
You will need to set SUBJECTS_DIR to some other path not under /Applications 
where you can normally write to as your userid, e.g., 
$ mkdir $HOME/subjects$ export SUBJECTS_DIR=$HOME/subjects
- R.

On Jul 31, 2023, at 18:16, Alan Francis  
wrote:External Email - Use 
CautionHi Doug et al,I recently 
moved from Linux to MAC OS running Ventura.. When I run the recon-all, it gives 
me this message:“mri_compute_overlap” cannot be opened because the developer 
cannot be verified.The help given at the FS website is for previous MAC 
versions. Ventura does not allow what is shown on the website.Any 
suggestions?Thanks,Alan-- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|Alan
 N. Francis PhDAssistant Professor of NeuroscienceInstitute of 
NeuroscienceUniversity of Texas, School of MedicineRio Grande 
ValleyTexas.                 
                      
                      
                      
                      
  ___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://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
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.