[Freesurfer] Creating a seed sphere using MNI coordinate

[Addison, Reuben]

  1.  I am planning to add a seed sphere 6mm cortical and 4 millimeters 
subcortical and I want to do this with Fsfast using given MNI coordinates from 
a previous study. I am wondering if there is a command on fsfast to achieve 
that, I have gone through the connectivity analysis but couldn't quite figure a 
way to do that.

  1.   Also I want to add a covariate (behavioural score) to my second level 
connectivity map. I want to use fsfast for consistency sake. If I can be 
pointed to the command it will be very helpful.

Thanks,
Reuben N. Addison
Postdoctoral Fellow
Brain Recovery Lab
MGH Institute of Health Professions
Charlestown Navy Yard | 36 1st Avenue, Boston MA 02129


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Re: [Freesurfer] [EXTERNAL] Re: Error while testing FS version 5.1

[fsbuild]

External Email - Use Caution

You could try running FS 5.1 on Ubuntu 12 using either a container or VM, but 
I’m not aware of a container with Freesurfer 5.1 already installed.
I would try the VirtualBox VM with Freesurfer 5.3 and see if that works. 
 That is a known to be good image of the OS with everything installed for 
at least FS 5.3 to run.   You could first make a snapshot of the VM and 
then try installing FS 5.1 in it and see if it works.  If you have IT 
staff, they should be able to help you with doing this if you are not familiar 
with VirtualBox.

- R.
On Oct 5, 2022, at 15:07, leema_mur...@eisai.com 
wrote:External Email - Use 
CautionThank you so much for a 
detailed explanation. I have never tested FS 5.1 previously. This is my first 
time testing this version in a docker container. I’m not sure what older 
version of OS that should be used. Is there a docker base image available for 
FS 5.1 like it’s there for FS 7.2.. Regards,Leema From: fsbuild 
 Sent: Wednesday, October 5, 2022 2:54 
PMTo: freesur...@nmr.mgh..harvard.eduCc: Leema Krishna Murali 
Subject: Re: [Freesurfer] [EXTERNAL] Re: 
Error while testing FS version 5..1 Security First: External email, 
use caution clicking links or opening attachments.It looks like you are running 
into undefined symbols when running on Ubuntu 16.   You may need to use an 
older version of the OS.  I say that because we have an Ubuntu 12 VM 
with Freesurfer 5.3 that runs on VirtualBox available from MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
behttps://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full..vdi.gz ;
   And FS 5.1 predates FS 5.3. We post a note you should be aware of 
about changing the operating system you run freesurfer on: Important 
Note: When processing a group of subjects for your study, it is essential 
to process all your subjects with the same version of FreeSurfer, on the same 
OS platform and vendor, and for safety, even the same version of the OS. While 
we continue to work to ensure that results match across platforms, there are 
none-the-less system-level libraries that are OS dependent. An exception to 
this rule is that you may view and edit files across any platform or version, 
and run some post-processing tools (outside the recon-all stream) if you check 
with us first (for instance you may run the longitudinal processing with newer 
versions). I interpret that to mean you should try and run FS 5.1 on the 
version of the OS you previously ran it on.  Otherwise, you may not get 
the same floating point output from running your existing test 
subjects. So as Paul mentioned, you can use a container, a virtual machine 
(VM) or any virtualization scheme to run FS 5.1 on am older version of the OS, 
and host the container, VM, etc. on Ubuntu 18.   Ubuntu Linux has its own 
built-in virtualization called QEMU.   I would at least start with 
whatever OS you previously ran FS 5.1 on as the reference. - R. On 
Oct 5, 2022, at 
14:36, leema_mur...@eisai.com wrote: External
 Email - Use Caution Hi 
Paul, Thank you for your response. I did try running FreeSurfer inside a 
docker derived from Ubuntu 16.04. Now there is no license invalid error. But 
I’m facing another error with regard to Segmentation. Please find the below 
screenshot..  Thank 
you,Leema From: freesurfer-boun...@nmr.mgh.harvard.edu  On
 Behalf Of Wighton, PaulSent: Wednesday, October 5, 2022 11:30 
AMTo: freesur...@nmr.mgh.harvard.eduSubject: [EXTERNAL] Re: 
[Freesurfer] Error while testing FS version 5.1 Security 
First: External email, use caution clicking links or opening 
attachments.Hi Leema, This is a known issue.  It has to do with the 
behaviour of the crypt() function provided by glibc, which has changed in more 
recent versions of ubuntu.  We don't have a solution for it at this time, 
unfortunately. If you downgrade to ubuntu version 16.04 (glibc v2.23) the 
license mechanism should work, or you could upgrade your version of 
FreeSurfer.  If neither of those options are possible, you could run 
FreeSurfer inside a docker or singularity container derived from ubuntu 
16.04. -Paul From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf 
of leema_mur...@eisai.comSent: Wednesday,
 October 5, 2022 8:43 
AMTo: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer]
 FW: Error while testing FS version 
5.1 External Email - Use 
CautionHello FreeSurfer 
Developers, I’m trying to use Freesurfer version 5.1 for my work. I get 
errors based on invalid license even though I have provided the right license 
within $FREESURFER_HOME/.license Is there a specific way to define the 
license file for 5.1 version. I hav

Re: [Freesurfer] [EXTERNAL] Re: Error while testing FS version 5.1

[Leema_Murali]

External Email - Use Caution

Thank you so much for a detailed explanation. I have never tested FS 5.1 
previously. This is my first time testing this version in a docker container. 
I’m not sure what older version of OS that should be used. Is there a docker 
base image available for FS 5.1 like it’s there for FS 7.2.

Regards,
Leema

From: fsbuild 
Sent: Wednesday, October 5, 2022 2:54 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Leema Krishna Murali 
Subject: Re: [Freesurfer] [EXTERNAL] Re: Error while testing FS version 5.1

Security First: External email, use caution clicking links or opening 
attachments.
It looks like you are running into undefined symbols when running on Ubuntu 16. 
  You may need to use an older version of the OS.  I say that because we have 
an Ubuntu 12 VM with Freesurfer 5.3 that runs on VirtualBox available from 
https://secure-web.cisco.com/1Z8V5MA6RVUcl116-PIV00OZzIY_Z1HFtQRNdPVTd18pxf2bAZ50OBdCVVNIxzsxvr_ZRp6BUNcpu-4ceDpV_JbF2SZZ5jrao7nDq6JVf5RCNlzadUSpWZ0bRqKevfxVMWNmw5wHbT9D9QxYm0bcjlPaaCaremOjLOisAjdZC-VXv3DBj5iocLVz4YvK8kL9N0K7l6I9JDXrl3ldF22chro-q9noFvJcu0Eue_T5z569EgQNF-dSmOJp_FiOn6Vjlxy9Gnd2ybeuxC4h_KPmVdV1i98MXLfE7pOSvQGg2iMjF2PqiIlk7LbkBzm2QEE0IttumxjkusJEBpbUnIK3--g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F5.3.0%2Ffreesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full..vdi.gz
And FS 5.1 predates FS 5.3.

We post a note you should be aware of about changing the operating system you 
run freesurfer on:

Important Note: When processing a group of subjects for your study, it is 
essential to process all your subjects with the same version of FreeSurfer, on 
the same OS platform and vendor, and for safety, even the same version of the 
OS. While we continue to work to ensure that results match across platforms, 
there are none-the-less system-level libraries that are OS dependent. An 
exception to this rule is that you may view and edit files across any platform 
or version, and run some post-processing tools (outside the recon-all stream) 
if you check with us first (for instance you may run the longitudinal 
processing with newer versions).

I interpret that to mean you should try and run FS 5.1 on the version of the OS 
you previously ran it on.  Otherwise, you may not get the same floating point 
output from running your existing test subjects.

So as Paul mentioned, you can use a container, a virtual machine (VM) or any 
virtualization scheme to run FS 5.1 on am older version of the OS, and host the 
container, VM, etc. on Ubuntu 18.   Ubuntu Linux has its own built-in 
virtualization called QEMU.   I would at least start with whatever OS you 
previously ran FS 5.1 on as the reference.

- R.

On Oct 5, 2022, at 14:36, leema_mur...@eisai.com 
wrote:

External Email - Use Caution

Hi Paul,

Thank you for your response. I did try running FreeSurfer inside a docker 
derived from Ubuntu 16.04. Now there is no license invalid error. But I’m 
facing another error with regard to Segmentation. Please find the below 
screenshot.



Thank you,
Leema

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Wighton, Paul
Sent: Wednesday, October 5, 2022 11:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXTERNAL] Re: [Freesurfer] Error while testing FS version 5.1

Security First: External email, use caution clicking links or opening 
attachments.
Hi Leema,

This is a known issue.  It has to do with the behaviour of the crypt() function 
provided by glibc, which has changed in more recent versions of ubuntu.  We 
don't have a solution for it at this time, unfortunately.

If you downgrade to ubuntu version 16.04 (glibc v2.23) the license mechanism 
should work, or you could upgrade your version of FreeSurfer.  If neither of 
those options are possible, you could run FreeSurfer inside a docker or 
singularity container derived fro

Re: [Freesurfer] [EXTERNAL] Re: Error while testing FS version 5.1

[fsbuild]

External Email - Use Caution

It looks like you are running into undefined symbols when running on Ubuntu 16. 
  You may need to use an older version of the OS.  I say that because 
we have an Ubuntu 12 VM with Freesurfer 5.3 that runs on VirtualBox 
available 
from https://secure-web.cisco.com/1OwyjJ1rTGJ_2TzRiqQk1sQK1uz8hOtzOw5oFxzSzAGWIbR-Yz-_ssSXyRXYlvsdeqRQ2Fy7Yfu-WMoy__RqtPCm2OEroskdi8rCumoQnjWrZmlPCRzQLnNJ-tvoPXyeEKj2uT61s27ya-32h-g-U-uYYpl6Ty-vGmBGbyZ9XZau0WiekR8U-Mbv5JcZ5DdvMGQfNIMmCEk29Vzyk6NMouOBUVn9Ye5vZiz47GM1ap4sAsNyYeEFpCPRFaAOuntmVYJ6cgL1QU3U9L9Uublr2b1RDr5Y0a1sQIcGcLuryQE-ZWFN2kZJMB63of7BqtP0EtubB-zCtigJbKftCIiDHvQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F5.3.0%2Ffreesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz%26nbsp;
   And FS 5.1 predates FS 5.3.
We post a note you should be aware of about changing the operating system you 
run freesurfer on:
Important Note: When processing a group of subjects for your study, it is 
essential to process all your subjects with the same version of FreeSurfer, on 
the same OS platform and vendor, and for safety, even the same version of the 
OS. While we continue to work to ensure that results match across platforms, 
there are none-the-less system-level libraries that are OS dependent. An 
exception to this rule is that you may view and edit files across any platform 
or version, and run some post-processing tools (outside the recon-all stream) 
if you check with us first (for instance you may run the longitudinal 
processing with newer versions).
I interpret that to mean you should try and run FS 5.1 on the version of the OS 
you previously ran it on.  Otherwise, you may not get the same floating 
point output from running your existing test subjects.
So as Paul mentioned, you can use a container, a virtual machine (VM) or any 
virtualization scheme to run FS 5.1 on am older version of the OS, and host the 
container, VM, etc. on Ubuntu 18.   Ubuntu Linux has its own built-in 
virtualization called QEMU.   I would at least start with whatever OS you 
previously ran FS 5.1 on as the reference.

- R.

On Oct 5, 2022, at 14:36, leema_mur...@eisai.com 
wrote:External Email - Use 
CautionHi Paul, Thank you 
for your response. I did try running FreeSurfer inside a docker derived from 
Ubuntu 16.04. Now there is no license invalid error. But I’m facing another 
error with regard to Segmentation. Please find the below 
screenshot.  Thank 
you,Leema From: freesurfer-boun...@nmr.mgh.harvard.edu  On
 Behalf Of Wighton, PaulSent: Wednesday, October 5, 2022 11:30 
AMTo: freesur...@nmr.mgh.harvard.eduSubject: [EXTERNAL] Re: 
[Freesurfer] Error while testing FS version 5.1 Security 
First: External email, use caution clicking links or opening 
attachments.Hi Leema, This is a known issue.  It has to do with the 
behaviour of the crypt() function provided by glibc, which has changed in more 
recent versions of ubuntu.  We don't have a solution for it at this time, 
unfortunately. If you downgrade to ubuntu version 16.04 (glibc v2.23) the 
license mechanism should work, or you could upgrade your version of 
FreeSurfer.  If neither of those options are possible, you could run 
FreeSurfer inside a docker or singularity container derived from ubuntu 
16.04. -Paul From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf 
of leema_mur...@eisai.comSent: Wednesday,
 October 5, 2022 8:43 
AMTo: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer]
 FW: Error while testing FS version 
5.1 External Email - Use 
CautionHello FreeSurfer 
Developers, I’m trying to use Freesurfer version 5.1 for my work. I get 
errors based on invalid license even though I have provided the right license 
within $FREESURFER_HOME/.license Is there a specific way to define the 
license file for 5.1 version. I have been using the latest version before and I 
had just added the license.txt with $FREESURFER_HOME. Please can anyone 
help me to troubleshoot this  issue. Platform: Ubuntu 18.04Freesurfer 
version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0recon-all.log: see 
attached  Looking forward for you 
reply. Thank you,Leema[This e-mail message may contain privileged, 
confidential and/or proprietary information of Eisai. If you believe that it 
has been sent to you in error, please contact the sender immediately and delete 
the message including any attachments, without copying, using, or distributing 
any of the information contained therein. This e-mail message should not be 
interpreted to include a digital or electronic signature that can be used to 
authenticate an agreement, contract or other legal document, nor to reflect an 
intention to be bound to any legally-binding agreement or 
contract.] ___Fr

Re: [Freesurfer] [EXTERNAL] Re: Error while testing FS version 5.1

[Leema_Murali]

External Email - Use Caution

Hi Paul,

Thank you for your response. I did try running FreeSurfer inside a docker 
derived from Ubuntu 16.04. Now there is no license invalid error. But I'm 
facing another error with regard to Segmentation. Please find the below 
screenshot.

[cid:image002.png@01D8D8C7.CB8C2300]

Thank you,
Leema

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Wighton, Paul
Sent: Wednesday, October 5, 2022 11:30 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXTERNAL] Re: [Freesurfer] Error while testing FS version 5.1

Security First: External email, use caution clicking links or opening 
attachments.
Hi Leema,

This is a known issue.  It has to do with the behaviour of the crypt() function 
provided by glibc, which has changed in more recent versions of ubuntu.  We 
don't have a solution for it at this time, unfortunately.

If you downgrade to ubuntu version 16.04 (glibc v2.23) the license mechanism 
should work, or you could upgrade your version of FreeSurfer.  If neither of 
those options are possible, you could run FreeSurfer inside a docker or 
singularity container derived from ubuntu 16.04.

-Paul


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of leema_mur...@eisai.com 
mailto:leema_mur...@eisai.com>>
Sent: Wednesday, October 5, 2022 8:43 AM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] FW: Error while testing FS version 5.1


External Email - Use Caution

Hello FreeSurfer Developers,



I'm trying to use Freesurfer version 5.1 for my work. I get errors based on 
invalid license even though I have provided the right license within 
$FREESURFER_HOME/.license



Is there a specific way to define the license file for 5.1 version. I have been 
using the latest version before and I had just added the license.txt with 
$FREESURFER_HOME.



Please can anyone help me to troubleshoot this  issue.



Platform: Ubuntu 18.04

Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0

recon-all.log: see attached



[cid:image003.png@01D8D8C7.CB8C2300]



Looking forward for you reply.



Thank you,

Leema


[This e-mail message may contain privileged, confidential and/or proprietary 
information of Eisai. If you believe that it has been sent to you in error, 
please contact the sender immediately and delete the message including any 
attachments, without copying, using, or distributing any of the information 
contained therein. This e-mail message should not be interpreted to include a 
digital or electronic signature that can be used to authenticate an agreement, 
contract or other legal document, nor to reflect an intention to be bound to 
any legally-binding agreement or contract.]
___
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 
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Re: [Freesurfer] Error while testing FS version 5.1

[Wighton, Paul]

Hi Leema,

This is a known issue.  It has to do with the behaviour of the crypt() function 
provided by glibc, which has changed in more recent versions of ubuntu.  We 
don't have a solution for it at this time, unfortunately.

If you downgrade to ubuntu version 16.04 (glibc v2.23) the license mechanism 
should work, or you could upgrade your version of FreeSurfer.  If neither of 
those options are possible, you could run FreeSurfer inside a docker or 
singularity container derived from ubuntu 16.04.

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of leema_mur...@eisai.com 

Sent: Wednesday, October 5, 2022 8:43 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] FW: Error while testing FS version 5.1


External Email - Use Caution

Hello FreeSurfer Developers,



I’m trying to use Freesurfer version 5.1 for my work. I get errors based on 
invalid license even though I have provided the right license within 
$FREESURFER_HOME/.license



Is there a specific way to define the license file for 5.1 version. I have been 
using the latest version before and I had just added the license.txt with 
$FREESURFER_HOME.



Please can anyone help me to troubleshoot this  issue.



Platform: Ubuntu 18.04

Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0

recon-all.log: see attached



[cid:image001.png@01D8D895.A24160F0]



Looking forward for you reply.



Thank you,

Leema


[This e-mail message may contain privileged, confidential and/or proprietary 
information of Eisai. If you believe that it has been sent to you in error, 
please contact the sender immediately and delete the message including any 
attachments, without copying, using, or distributing any of the information 
contained therein. This e-mail message should not be interpreted to include a 
digital or electronic signature that can be used to authenticate an agreement, 
contract or other legal document, nor to reflect an intention to be bound to 
any legally-binding agreement or contract.]
___
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] FW: Error while testing FS version 5.1

[Leema_Murali]

External Email - Use Caution

Hello FreeSurfer Developers,

I'm trying to use Freesurfer version 5.1 for my work. I get errors based on 
invalid license even though I have provided the right license within 
$FREESURFER_HOME/.license

Is there a specific way to define the license file for 5.1 version. I have been 
using the latest version before and I had just added the license.txt with 
$FREESURFER_HOME.

Please can anyone help me to troubleshoot this  issue.

Platform: Ubuntu 18.04
Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
recon-all.log: see attached

[cid:image001.png@01D8D895.A24160F0]

Looking forward for you reply.

Thank you,
Leema


[This e-mail message may contain privileged, confidential and/or proprietary 
information of Eisai. If you believe that it has been sent to you in error, 
please contact the sender immediately and delete the message including any 
attachments, without copying, using, or distributing any of the information 
contained therein. This e-mail message should not be interpreted to include a 
digital or electronic signature that can be used to authenticate an agreement, 
contract or other legal document, nor to reflect an intention to be bound to 
any legally-binding agreement or contract.]


recon-all.log
Description: recon-all.log
___
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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. 

Re: [Freesurfer] Segmentation fault: 11

[fsbuild]

External Email - Use Caution

Hello Priya,
It could help to know,- the version of freesurfer you installed, e.g., the 
latest 7.3.2 release 
from https://secure-web.cisco.com/1zdcvVhqKzcbDdvruGd5f9eNe1UebLwxcHQNPPf-imCCfHdpe0i9n7VbHnkOmApVqwXLBFsNTr00VNAx6komIIAOhuIRk6xXYWHGaglPYJchE8a9lzlAQT29GiC1raPpbWVbt94mHKkuJR3TiY-OFK_tCBU51VFFu9uewTnFXNckvsZOBZI1xinXrvWXo4w5sVl8oWlaqCnq6Y7DwKhnZA1W8tAh_0WR1Dd5kz8GcHoj9sFXFkVoDX7T9CJHyRmQLOsEBtrXXnYLMPFFrjKkqrgu3pegmOSzp28R-xM-z7A1a1dzarbK0-CzqxWJ0cOGPevrxtZTKgyk40s-Py98MTA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads-
 if you used the pkg installer 
file, https://secure-web.cisco.com/1kDieI9mdZudxJbpCFL6WFWngUIQhFugSuxCTUgxkN4I7zm6B97n6zFOzOXu7d603xiHK8yloksQA-mavSlbntpXNUVUyEt2IxFBqjbp6OUtHz3SjeZS5qpUI6EggsHyDvJJtjDS4pbNTfvUdNJlUnJJnH_mRxv60AkjaADCX8b9l-VmjWA3FG7JYhgzwTRLXm9GPZsPTIU-e5UnobSwIR9tS1dOYAboIUCHNkEogDt9FoYYVBGSIsQo9Jee3atsYxSR64iJe60_iQ-NzWOFWqlewHJJ8H1DmEDFe3TDApSJWsPGzPXJUgiyGdPNG5elZR4By4jQUjMJHrLLS8l6s6Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.3.2%2Ffreesurfer-darwin-macOS-7.3.2.pkg-
 what version of MacOS you are running- if you are on an Intel Mac or a new Mac 
with an M1 or M2 chip.
Please make sure you have registered and obtained the freesurfer license.txt 
file by filling out the 
form, https://secure-web.cisco.com/1fpZEOUr_MAQGgEoaIOkzRF-3qUqa6N-GPoNFHsbrnuctCNmhc9id24leJoz6l_qPb6qchGVB28sc5TdXgeSKmsRlhcbWOsDymDubYiXzgDxPTbwBQjIbrztHG0NYp5bU7EFt6dP2ZtmHAXPyqGmnwaB3Ffo_ZayGhQjWhRKFoRyemOSV5sgNJ9PUqhmJ84MunQN_cVhc3ybjFpZSYLbvDcRyhWw-w3b9eFhc1I4S0QIOzL9x0y1bZXRQWztyGsc1epLYYkbUkt1_L7uLnyjQK1KVwy8jmpipmkQM3_wIYDODTLe2QlG_g039fO_c9J4D_EV7DNibbDR4B4r32eJrYQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fregistration.html
The thread you 
referenced, https://secure-web.cisco.com/1D0s4CKkxCu5d6CQKJUyf4knHMaxqpw-OaFbdce0DVPAKaX9_RQ-4wDkshtLmkg81ku3ximPzzeVVQkKFd7oGBdTVb2vtcZKh97LrioXea3Sz7D3G5Pov9ZvUq-qaDE3hFFPtBrQOQwC2rNLEnqex3OEbopWB9_cxjliyD0lsJD6JPEIUCAnAjnjNFy2fxfQC77hKBoDRLqa3hs_HlnwLqMJdlTujxDGrzj9cL59p24ppVlrzg64XgLi3-jAZwc4-HXyYaUIB0t3Smao8B7yPSzb6gHxA5UZhrjOsGMKZBBdPqiHG9pkVDZEftp3zgOIK/https%3A%2F%2Fneurostars.org%2Ft%2Fproblem-installing-freesurfer-in-mac%2F20552%2F21,
 showed the crash went away for a user with a MacBook Pro if they unplugged 
their external monitor.  This is - or at least was - a known problem with 
a 2nd monitor causing a segfault when trying to run some graphics programs. 
 So try unplugging any external monitor if you are using a Mac laptop.
I would try explicitly running the bash shell in your terminal window, but 
typing “bash” at the terminal prompt.  You should then see the output,
$ bash
The default interactive shell is now zsh.
To update your account to use zsh, please run `chsh -s /bin/zsh`.
For more details, please visit 
https://secure-web.cisco.com/1weI0CySFCptz62exS6gCfA2Ymaa7qVQzIZURPdDJ1Yz2dGxXIspkZGB_bUF7bkIFa3SThCs1dYsJwb0g_pcZW825OZ72WiPjcT6_-lQk7bCxJRkhJqF31WXDnFEUusUDjyR6j2iYFIkYSDykxrl9xXbk1ccoVsyf1kR1ElUppfBf-JiSRggqQdhsUMq_wCisCD-Do1HGhK1NeljTcTx6m9iT5Q8W0rwhyXf1GzLdQb9Ln8jMKhV-UNUtiy2QQii88TUkIIZBENPD5fchnBWfZOBAj58YzZ90EhP8nLAIusrH8tMKpmIjHAkpyhETYSCdKCc_3CAybPXYV_ONJ33YkQ/https%3A%2F%2Fsupport.apple.com%2Fkb%2FHT208050.userid%40hostname%3A%7E%26gt;
You can then set FS_LICENSE in your environment to point to the license.txt 
file.  You can put license.txt in your home directory, e.g., wherever that 
path is,

userid@hostname:~> echo $HOME/Users/priya
userid@hostname:~> export 
FS_LICENSE=$HOME/license.txtuserid@hostname:~> cat $FS_LICENSE< output 
deleted - just make sure the environment variable points to license.txt >
Then setup the fressurfer environment, e.g., for the 7.3.2 release installed 
with the .pkg file,
userid@hostname:~> export 
FREESURFER_HOME=/Applications/freesurfer/7.3.2userid@hostname:~> source 
$FREESURFER_HOME/SetUpFreeSurfer.sh
 freesurfer-darwin-macOS-7.3.2-20220803-878457d 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.3.2
FSFAST_HOME       /Users/developer/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Users/developer/freesurfer/subjects
TUTORIAL_DATA     /Users/developer/tutorial_data
MNI_DIR         
  /Users/developer/freesurfer/mni
WARNING: /Users/developer/freesurfer/fsl_507/bin does not exist.
FSL_DIR         
  /Users/developer/freesurfer/fsl_507

userid@hostname:~> which freeview/Applications/freesurfer/7.3.2/bin/freeview
… try running freeview with no argument to see if it brings up an 
empty window …
userid@hostname:~> freeview
… try displaying a simple volume …
userid@hostname:~> freeview $SUBJECTS_DIR/bert/mri/brain.mgz
Let us know how it goes.
- R.
On Oct 5, 2022, at 03:11, priya padma  
wrote:External Email - Use 
CautionHello Team,I just 
installed freesurfer and freeview using the methods mentioned 
in MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.

[Freesurfer] Password for FreeSurfer VirtualBox VM Images

[zhenyi]

External Email - Use Caution

Dear FreeSurfer experts,

I would like the password to unzip the virtual machine 
FS_7_2_0_ubuntu_18_04_06.ova.7z. Thanks a lot.

Best regards___
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The information in this e-mail is intended only for the person to whom it is 
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[Freesurfer] Segmentation fault: 11

[priya padma]

External Email - Use Caution

Hello Team,

I just installed freesurfer and freeview using the methods mentioned in
https://secure-web.cisco.com/1oeEk1V3fGDlcuYEIm1RFYCYdQcU2m3TJysRGz7NAzZIOMDfxJiOPbas0gR6C45O_k9X6OvLE4pS75bwDoZy4yIzpxK5rduxKwxnHn7m8NEYSw4zXC5joOtwNk5Ms6X54nQoAn7rrCj9BiT1MW3U0nvSPBWGAHn1-KKiJGeORXiIxTTaJU2IhmN_cryZ288yejqNjTtt-OGUhFKw0-g8EuAc_NNBv7FyYimFnE60vT3lXwRS9S8OoUQOq9smu1FATiEsgK1lbDVds_iBqLgQy9QAccg056gs1_IXcIHxwX41K6s2GOsaYfmb4qiLkMLgB/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2F%2FFS7_mac
the installation was successful and after creating the environment the
freeview also opened but whenever I open any volume, freeview crashes and I
get an error saying line 2:  6736 Segmentation fault: 11
$FREESURFER_HOME/Freeview.app/Contents/MacOS/freeview
"$@"

I followed the thread
https://secure-web.cisco.com/1Xm7JHZ-l0iAQ6540xdJyuY8nR4ldJU2U31IejPX9O93yncEj0bj1Zlci1unp989Xa1G5UcsaEluZenniTs3pmbfVzbWdlTyRGxygKzrb86U7QdD-UXmQdHNkER0_iq0KmQ_4wz4BHdolR7Lhflv_Rxbki0GzeYFxpyj_cErj7IlEK3dJVVzP9fzpqIzF4tv3uZ9aTOO-VftQSyntsUFB5ytO4PQK0prMhfzK6qoiwvruqin7GEO3_XveaXxgqgHNYMkkZ1IvWRmWhHlIHUPYlPZXOjAN_VUTk0YUgZSBCFd6bEAzZ1UhLOXddXOAOyEQ/https%3A%2F%2Fneurostars.org%2Ft%2Fproblem-installing-freesurfer-in-mac%2F20552%2F2
and tried to move the terminal to the main laptop screen but still I get
the same error. I am unable to open the sample data given along with
freesurfer.

Could you help me with this issue?

-- 
Best Regards
Padma Priya
*AI Developer *

*PhenoMx, Inc.*
*pr...@phenomx.ai  | (+82)10-5405-2685*
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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.