Re: [Freesurfer] FreeSurfer v5.1

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FreeSurfer v5.1

fsbuild

12 Aug 2020 12 Aug '20

6:14 p.m.

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Hello Jessica,

I believe the environment variable FREESURFER_HOME should point to where the license.txt file lives.  That is set when you source the freesurfer setup script, e.g., SetUpFreeSurfer.sh, in the terminal window.

You can see the wiki page here for the 5.3 setup,

https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall5.3

It looks like the message indicates it is looking for ".license.txt" and not "license.txt"

So in a terminal window you could try the following. First make sure FREESURFER_HOME is set,

$ echo $FREESURFER_HOME

/Applications/freesurfer

Then take the  "license.txt" file that was emailed to you  and copy it into $FREESURFER_HOME, e..g.

$ cp -p -f license.txt $FREESURFER_HOME/.

Now also make a copy of it there as ".license" - no harm in having it named both ways under $FREESURFER_HOME

$ cd $FREESURFER_HOME

$ cp -p -f license.txt  .license.txt

.... then try running things again.

- R.

Hua, Jessica August 12, 2020 at 17:13

        External Email - Use Caution        

Hi FreeSurfer,

I was able to find the older versions of FreeSurfer and download v5.1. I am trying to run recon-all and am running into this issue:

ERROR: FreeSurfer license file /Applications/freesurfer/.license not found.   If you are outside the NMR-Martinos Center,   go to http://surfer.nmr.mgh.harvard.edu to   get a valid license file (it's free).   If you are inside the NMR-Martinos Center,   make sure to source the standard environment.

I went online and filled out information to get a license.  I then added the license.txt file to the Applications/freesurfer folder, but I am still getting the same error message.  How do I get a .license file? I checked to unhide hidden files, and there is no .license file..

Jessica

From: Hua, Jessica

Sent: Wednesday, August 12, 2020 12:36 PM

To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>

Subject: FreeSurfer v5.1  

Hi FreeSurfer,

To be consistent with old analyses, I need to process my data using FreeSurfer v5.1 on my Mac.  Do you know where I can find the link to install v5.1?

Best,

Jessica Hua

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Hua, Jessica August 12, 2020 at 15:36

        External Email - Use Caution        

Hi FreeSurfer,

To be consistent with old analyses, I need to process my data using FreeSurfer v5.1 on my Mac.  Do you know where I can find the link to install v5.1?

Best,

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

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Hua, Jessica

12 Aug 12 Aug

6:27 p.m.

New subject: FreeSurfer v5.1 {Disarmed}

External Email - Use Caution

Hi FreeSurfer,

I did the below steps, and I am still getting the same error message.

ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.

I checked, and my FreeSurfer file home folder is Applications/freesurfer. And in that folder, I now have a license.txt file as well as a .license.txt file.

I have attached the error log in case helpful.

Jessica Hua ________________________________ From: fsbuild fsbuild@contbay.com Sent: Wednesday, August 12, 2020 3:14 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Hua, Jessica Jessica.Hua@ucsf.edu Subject: Re: [Freesurfer] FreeSurfer v5.1

Hello Jessica,

I believe the environment variable FREESURFER_HOME should point to where the license.txt file lives. That is set when you source the freesurfer setup script, e.g., SetUpFreeSurfer.sh, in the terminal window.

You can see the wiki page here for the 5.3 setup, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall5.3 https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_DownloadAndInstall5.3&d=DwQFaQ&c=iORugZls2LlYyCAZRB3XLg&r=O7y8UebexwRWyF1th93__qgMOjQ2C85yHAGleU3LVgQ&m=dnbMmPzQjzsvKU8GmdlZcOlyQ8o-eAu8D0P7vUA3VN4&s=w8y-0_JGO7m_i508I5ragfcwm0qCrbk2ZO0d65JsYHc&e=

It looks like the message indicates it is looking for ".license.txt" and not "license.txt"

So in a terminal window you could try the following.

First make sure FREESURFER_HOME is set,

$ echo $FREESURFER_HOME /Applications/freesurfer

Then take the "license.txt" file that was emailed to you and copy it into $FREESURFER_HOME, e.g.

$ cp -p -f license.txt $FREESURFER_HOME/.

Now also make a copy of it there as ".license" - no harm in having it named both ways under $FREESURFER_HOME

$ cd $FREESURFER_HOME $ cp -p -f license.txt .license.txt

... then try running things again.

- R. Hua, Jessicamailto:Jessica.Hua@ucsf.edu August 12, 2020 at 17:13

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Hi FreeSurfer,

I was able to find the older versions of FreeSurfer and download v5.1. I am trying to run recon-all and am running into this issue:

ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu&d=DwQFaQ&c=iORugZls2LlYyCAZRB3XLg&r=O7y8UebexwRWyF1th93__qgMOjQ2C85yHAGleU3LVgQ&m=dnbMmPzQjzsvKU8GmdlZcOlyQ8o-eAu8D0P7vUA3VN4&s=4eDMCpc5qiu7jm_VpgsYGEztIcr7LQ5IrSgx937xCgM&e= to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.

I went online and filled out information to get a license. I then added the license.txt file to the Applications/freesurfer folder, but I am still getting the same error message. How do I get a .license file? I checked to unhide hidden files, and there is no .license file.

Jessica ________________________________ From: Hua, Jessica Sent: Wednesday, August 12, 2020 12:36 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: FreeSurfer v5.1

Hi FreeSurfer,

To be consistent with old analyses, I need to process my data using FreeSurfer v5.1 on my Mac. Do you know where I can find the link to install v5.1?

Best,

Jessica Hua _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwQFaQ&c=iORugZls2LlYyCAZRB3XLg&r=O7y8UebexwRWyF1th93__qgMOjQ2C85yHAGleU3LVgQ&m=dnbMmPzQjzsvKU8GmdlZcOlyQ8o-eAu8D0P7vUA3VN4&s=m3vcPP-IPrTrqtP4aEjOeo8RrqyeHA1N7jJV7DM8bAE&e= Hua, Jessicamailto:Jessica.Hua@ucsf.edu August 12, 2020 at 15:36

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Hi FreeSurfer,

To be consistent with old analyses, I need to process my data using FreeSurfer v5.1 on my Mac. Do you know where I can find the link to install v5.1?

Best,

Tyler Ward

11:46 p.m.

New subject: FreeSurfer v5.1 {Disarmed}

External Email - Use Caution

Hi Jessica,

Freesurfer is actually looking for the file "/Applications/freesurfer/.license", excluding the file extension. You can simply remove the ".txt" extension from the file name such as with:

/$ mv /Applications/freesurfer/.license.txt /Applications/freesurfer/.license/

On 8/12/20 3:27 PM, Hua, Jessica wrote:

...

External Email - Use Caution

Hi FreeSurfer,

I did the below steps, and I am still getting the same error message.

ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.

I checked, and my FreeSurfer file home folder is Applications/freesurfer. And in that folder, I now have a license.txt file as well as a .license.txt file.

I have attached the error log in case helpful.

Jessica Hua

*From:* fsbuild fsbuild@contbay.com *Sent:* Wednesday, August 12, 2020 3:14 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Cc:* Hua, Jessica Jessica.Hua@ucsf.edu *Subject:* Re: [Freesurfer] FreeSurfer v5.1 Hello Jessica,

I believe the environment variable FREESURFER_HOME should point to where the license.txt file lives. That is set when you source the freesurfer setup script, e.g., SetUpFreeSurfer.sh, in the terminal window.

You can see the wiki page here for the 5.3 setup, *MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be* https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall5.3 https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_DownloadAndInstall5.3&d=DwQFaQ&c=iORugZls2LlYyCAZRB3XLg&r=O7y8UebexwRWyF1th93__qgMOjQ2C85yHAGleU3LVgQ&m=dnbMmPzQjzsvKU8GmdlZcOlyQ8o-eAu8D0P7vUA3VN4&s=w8y-0_JGO7m_i508I5ragfcwm0qCrbk2ZO0d65JsYHc&e=

It looks like the message indicates it is looking for ".license.txt" and not "license.txt"

So in a terminal window you could try the following.

First make sure FREESURFER_HOME is set,

$ echo $FREESURFER_HOME /Applications/freesurfer

Then take the "license.txt" file that was emailed to you and copy it into $FREESURFER_HOME, e.g.

$ cp -p -f license.txt $FREESURFER_HOME/.

Now also make a copy of it there as ".license" - no harm in having it named both ways under $FREESURFER_HOME

$ cd $FREESURFER_HOME $ cp -p -f license.txt .license.txt

... then try running things again.

R.

...
Hua, Jessica mailto:Jessica.Hua@ucsf.edu August 12, 2020 at 17:13

External Email - Use Caution

Hi FreeSurfer,

I was able to find the older versions of FreeSurfer and download v5.1. I am trying to run recon-all and am running into this issue:

ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to *MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be* http://surfer.nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu&d=DwQFaQ&c=iORugZls2LlYyCAZRB3XLg&r=O7y8UebexwRWyF1th93__qgMOjQ2C85yHAGleU3LVgQ&m=dnbMmPzQjzsvKU8GmdlZcOlyQ8o-eAu8D0P7vUA3VN4&s=4eDMCpc5qiu7jm_VpgsYGEztIcr7LQ5IrSgx937xCgM&e= to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.

I went online and filled out information to get a license. I then added the license.txt file to the Applications/freesurfer folder, but I am still getting the same error message. How do I get a .license file? I checked to unhide hidden files, and there is no .license file.

Jessica

*From:* Hua, Jessica *Sent:* Wednesday, August 12, 2020 12:36 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* FreeSurfer v5.1 Hi FreeSurfer,

To be consistent with old analyses, I need to process my data using FreeSurfer v5.1 on my Mac. Do you know where I can find the link to install v5.1?

Best,

Jessica Hua _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwQFaQ&c=iORugZls2LlYyCAZRB3XLg&r=O7y8UebexwRWyF1th93__qgMOjQ2C85yHAGleU3LVgQ&m=dnbMmPzQjzsvKU8GmdlZcOlyQ8o-eAu8D0P7vUA3VN4&s=m3vcPP-IPrTrqtP4aEjOeo8RrqyeHA1N7jJV7DM8bAE&e= Hua, Jessica mailto:Jessica.Hua@ucsf.edu August 12, 2020 at 15:36

External Email - Use Caution

Hi FreeSurfer,

To be consistent with old analyses, I need to process my data using FreeSurfer v5.1 on my Mac. Do you know where I can find the link to install v5.1?

Best,

Jessica Hua _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwQFaQ&c=iORugZls2LlYyCAZRB3XLg&r=O7y8UebexwRWyF1th93__qgMOjQ2C85yHAGleU3LVgQ&m=dnbMmPzQjzsvKU8GmdlZcOlyQ8o-eAu8D0P7vUA3VN4&s=m3vcPP-IPrTrqtP4aEjOeo8RrqyeHA1N7jJV7DM8bAE&e=

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

Hua, Jessica

13 Aug 13 Aug

1:03 a.m.

New subject: FreeSurfer v5.1 {Disarmed}

External Email - Use Caution

Thanks, that did the trick! ________________________________ From: Tyler Ward tjward@berkeley.edu Sent: Wednesday, August 12, 2020 8:46 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Cc: Hua, Jessica Jessica.Hua@ucsf.edu Subject: Re: [Freesurfer] FreeSurfer v5.1 {Disarmed}

Hi Jessica,

Freesurfer is actually looking for the file "/Applications/freesurfer/.license", excluding the file extension. You can simply remove the ".txt" extension from the file name such as with:

$ mv /Applications/freesurfer/.license.txt /Applications/freesurfer/.license

On 8/12/20 3:27 PM, Hua, Jessica wrote:

External Email - Use Caution

Hi FreeSurfer,

I did the below steps, and I am still getting the same error message.

ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu&d=DwMD-g&c=iORugZls2LlYyCAZRB3XLg&r=O7y8UebexwRWyF1th93__qgMOjQ2C85yHAGleU3LVgQ&m=tD0j6QcjYLNZjmvuairLO3aPlX76sbiD0aDlSjsPChM&s=a8Iyk3jjY_OLFL5pRBlkbxn-IyDSn_VC79j7yWHZ4Ew&e= to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.

I checked, and my FreeSurfer file home folder is Applications/freesurfer. And in that folder, I now have a license.txt file as well as a .license.txt file.

I have attached the error log in case helpful.

Jessica Hua ________________________________ From: fsbuild fsbuild@contbay.com mailto:fsbuild@contbay.com Sent: Wednesday, August 12, 2020 3:14 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Cc: Hua, Jessica Jessica.Hua@ucsf.edu mailto:Jessica.Hua@ucsf.edu Subject: Re: [Freesurfer] FreeSurfer v5.1

Hello Jessica,

I believe the environment variable FREESURFER_HOME should point to where the license.txt file lives. That is set when you source the freesurfer setup script, e.g., SetUpFreeSurfer.sh, in the terminal window.

You can see the wiki page here for the 5.3 setup, MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall5.3 https://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_DownloadAndInstall5.3&d=DwQFaQ&c=iORugZls2LlYyCAZRB3XLg&r=O7y8UebexwRWyF1th93__qgMOjQ2C85yHAGleU3LVgQ&m=dnbMmPzQjzsvKU8GmdlZcOlyQ8o-eAu8D0P7vUA3VN4&s=w8y-0_JGO7m_i508I5ragfcwm0qCrbk2ZO0d65JsYHc&e=

It looks like the message indicates it is looking for ".license.txt" and not "license.txt"

So in a terminal window you could try the following.

First make sure FREESURFER_HOME is set,

$ echo $FREESURFER_HOME /Applications/freesurfer

Then take the "license.txt" file that was emailed to you and copy it into $FREESURFER_HOME, e.g.

$ cp -p -f license.txt $FREESURFER_HOME/.

Now also make a copy of it there as ".license" - no harm in having it named both ways under $FREESURFER_HOME

$ cd $FREESURFER_HOME $ cp -p -f license.txt .license.txt

... then try running things again.

- R. Hua, Jessicamailto:Jessica.Hua@ucsf.edu August 12, 2020 at 17:13

External Email - Use Caution

Hi FreeSurfer,

I was able to find the older versions of FreeSurfer and download v5.1. I am trying to run recon-all and am running into this issue:

ERROR: FreeSurfer license file /Applications/freesurfer/.license not found. If you are outside the NMR-Martinos Center, go to MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be http://surfer.nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v2/url?u=http-3A__surfer.nmr.mgh.harvard.edu&d=DwQFaQ&c=iORugZls2LlYyCAZRB3XLg&r=O7y8UebexwRWyF1th93__qgMOjQ2C85yHAGleU3LVgQ&m=dnbMmPzQjzsvKU8GmdlZcOlyQ8o-eAu8D0P7vUA3VN4&s=4eDMCpc5qiu7jm_VpgsYGEztIcr7LQ5IrSgx937xCgM&e= to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment.

I went online and filled out information to get a license. I then added the license.txt file to the Applications/freesurfer folder, but I am still getting the same error message. How do I get a .license file? I checked to unhide hidden files, and there is no .license file.

Jessica ________________________________ From: Hua, Jessica Sent: Wednesday, August 12, 2020 12:36 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: FreeSurfer v5.1

Hi FreeSurfer,

To be consistent with old analyses, I need to process my data using FreeSurfer v5.1 on my Mac. Do you know where I can find the link to install v5.1?

Best,

Jessica Hua _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "urldefense.proofpoint.com" claiming to be https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwQFaQ&c=iORugZls2LlYyCAZRB3XLg&r=O7y8UebexwRWyF1th93__qgMOjQ2C85yHAGleU3LVgQ&m=dnbMmPzQjzsvKU8GmdlZcOlyQ8o-eAu8D0P7vUA3VN4&s=m3vcPP-IPrTrqtP4aEjOeo8RrqyeHA1N7jJV7DM8bAE&e= Hua, Jessicamailto:Jessica.Hua@ucsf.edu August 12, 2020 at 15:36

External Email - Use Caution

Hi FreeSurfer,

To be consistent with old analyses, I need to process my data using FreeSurfer v5.1 on my Mac. Do you know where I can find the link to install v5.1?

Best,

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.edu_mailman_listinfo_freesurfer&d=DwMD-g&c=iORugZls2LlYyCAZRB3XLg&r=O7y8UebexwRWyF1th93__qgMOjQ2C85yHAGleU3LVgQ&m=tD0j6QcjYLNZjmvuairLO3aPlX76sbiD0aDlSjsPChM&s=rkioK6hi3XHIeB7LVBCcM6GpSoyNfh2YBbCaEpY_txg&e=

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fsbuild
Hua, Jessica
Tyler Ward