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Hi Andrew

Thanks, cool, that looks like it worked. I'll run recon-all, check the logs and QA tools and let you know if I come across any issues.

Cheers James

On Sat, Sep 19, 2020 at 4:36 PM Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:

Hi James,

Try cd`ing to your home directory, then running:

curl https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/scripts/recon...

...

recon-all

sudo mv recon-all $FREESURFER_HOME/bin

best

Andrew

*From: *James Hartzell james.hartzell@gmail.com *Date: *Saturday, September 19, 2020 at 10:17 AM *To: *"Hoopes, Andrew" AHOOPES@mgh.harvard.edu, FS Help < freesurfer@nmr.mgh.harvard.edu> *Subject: *recon-all 7.1.1

•    External Email - Use Caution        *
  
  

Hi Andrew

Thanks for the suggestions. I removed freesurfer and reinstalled just 7.1.1.

When I try to run the original patch you suggested I still get permissions problems, even with sudo.

(base) jameshartzell@Jamess-MacBook-Pro ~ % which freesurfer /Applications/freesurfer/7.1.1/bin/freesurfer

(base) jameshartzell@Jamess-MacBook-Pro freesurfer % cd $FREESURFER_HOME/bin

(base) jameshartzell@Jamess-MacBook-Pro bin % sudo mv recon-all recon-all.backup

Password:

(base) jameshartzell@Jamess-MacBook-Pro bin % sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/scripts/recon...

...

recon-all

zsh: permission denied: recon-all

Here's hoping you can send another fix!

Cheers

James

--

James Hartzell, PhD (2x)

Donostia-San Sebatián, Spain

Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy

Center for Buddhist Studies, Columbia University, USA

Did you run `chmod +x` on the re-downloaded recon-all? Andrew

From: James Hartzell james.hartzell@gmail.com Date: Saturday, September 19, 2020 at 11:09 AM To: "Hoopes, Andrew" AHOOPES@mgh.harvard.edu Cc: FS Help freesurfer@nmr.mgh.harvard.edu Subject: Re: recon-all 7.1.1

External Email - Use Caution Hi Andrew

There's still some sort of problem:

(base) jameshartzell@Jamess-MacBook-Pro freesurfer % which freesurfer /Applications/freesurfer/7.1.1/bin/freesurfer

(base) jameshartzell@Jamess-MacBook-Pro freesurfer % recon-all -s $S -i $S....nii.gz -autorecon1 zsh: permission denied: recon-all zsh: permission denied: recon-all zsh: command not found: zsh:

Cheers James

On Sat, Sep 19, 2020 at 5:03 PM James Hartzell <james.hartzell@gmail.commailto:james.hartzell@gmail.com> wrote: Hi Andrew

Thanks, cool, that looks like it worked. I'll run recon-all, check the logs and QA tools and let you know if I come across any issues.

Cheers James

On Sat, Sep 19, 2020 at 4:36 PM Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> wrote: Hi James,

Try cd`ing to your home directory, then running:

curl https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/scripts/recon... > recon-all sudo mv recon-all $FREESURFER_HOME/bin

best Andrew

From: James Hartzell <james.hartzell@gmail.commailto:james.hartzell@gmail.com> Date: Saturday, September 19, 2020 at 10:17 AM To: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu>, FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: recon-all 7.1.1

External Email - Use Caution Hi Andrew

Thanks for the suggestions. I removed freesurfer and reinstalled just 7.1.1. When I try to run the original patch you suggested I still get permissions problems, even with sudo.

(base) jameshartzell@Jamess-MacBook-Pro ~ % which freesurfer /Applications/freesurfer/7.1.1/bin/freesurfer

(base) jameshartzell@Jamess-MacBook-Pro freesurfer % cd $FREESURFER_HOME/bin

(base) jameshartzell@Jamess-MacBook-Pro bin % sudo mv recon-all recon-all.backup Password:

(base) jameshartzell@Jamess-MacBook-Pro bin % sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/scripts/recon... > recon-all zsh: permission denied: recon-all

Here's hoping you can send another fix!

Cheers James

-- James Hartzell, PhD (2x) Donostia-San Sebatián, Spain Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy Center for Buddhist Studies, Columbia University, USA

-- James Hartzell, PhD (2x) Donostia-San Sebatián, Spain Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy Center for Buddhist Studies, Columbia University, USA

-- James Hartzell, PhD (2x) Donostia-San Sebatián, Spain Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy Center for Buddhist Studies, Columbia University, USA

Hi James,

If freesurfer was installed under root, you should prepend sudo to the command to make changes to the directory:

sudo FREESURFER_HOME=$FREESURFER_HOME fs_install_mcr R2014b

best Andrew

From: James Hartzell james.hartzell@gmail.com Date: Monday, September 21, 2020 at 10:49 AM To: "Hoopes, Andrew" AHOOPES@mgh.harvard.edu, FS Help freesurfer@nmr.mgh.harvard.edu Subject: Re: recon-all 7.1.1

External Email - Use Caution Hi Andrew

recon-all appears to have run successfully in 7.1.1, so thanks again for all the guidance.

I've just tried to install the matlab runtime for hipp, amyg, brainstem and thalamic segmentation, as per https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime

fs_install_mcr R2014b

the command finished, but indicated a problem with. final renaming requirement: "On the target computer, append the following to your DYLD_LIBRARY_PATH environment variable: /var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84/runtime/maci64:/var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84/sys/os/maci64:/var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84/bin/maci64:

(Sep 21, 2020 16:41:29) Exiting with status 0 (Sep 21, 2020 16:41:29) End - Successful. Finished mv: rename /var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84 to /Applications/freesurfer/7.1.1/MCRv84: Permission denied

Also, if you could provide guidance for the append step, that would be great.

Cheers

James

On Sat, Sep 19, 2020 at 4:17 PM James Hartzell <james.hartzell@gmail.commailto:james.hartzell@gmail.com> wrote: Hi Andrew

Thanks for the suggestions. I removed freesurfer and reinstalled just 7.1.1. When I try to run the original patch you suggested I still get permissions problems, even with sudo.

(base) jameshartzell@Jamess-MacBook-Pro ~ % which freesurfer /Applications/freesurfer/7.1.1/bin/freesurfer

(base) jameshartzell@Jamess-MacBook-Pro freesurfer % cd $FREESURFER_HOME/bin

(base) jameshartzell@Jamess-MacBook-Pro bin % sudo mv recon-all recon-all.backup Password:

(base) jameshartzell@Jamess-MacBook-Pro bin % sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/scripts/recon... > recon-all zsh: permission denied: recon-all

Here's hoping you can send another fix!

Cheers James

-- James Hartzell, PhD (2x) Donostia-San Sebatián, Spain Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy Center for Buddhist Studies, Columbia University, USA

-- James Hartzell, PhD (2x) Donostia-San Sebatián, Spain Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy Center for Buddhist Studies, Columbia University, USA

Hi James, please ignore that step. In fact, adding those matlab paths to your default DYLD_LIBRARY_PATH will most likely mess up freesurfer binaries in your environment. Andrew

From: James Hartzell james.hartzell@gmail.com Date: Tuesday, September 22, 2020 at 2:19 PM To: "Hoopes, Andrew" AHOOPES@mgh.harvard.edu Cc: FS Help freesurfer@nmr.mgh.harvard.edu Subject: Re: recon-all 7.1.1

External Email - Use Caution Hi Andrew Thanks, that works just fine. I'll see if I can figure out how to do the path append part--just something I'm not familiar with doing: (On the target computer, append the following to your DYLD_LIBRARY_PATH environment variable:

/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.LPxBFTBS/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.LPxBFTBS/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.LPxBFTBS/install-target/v84/bin/maci64:) Cheers James

On Tue, Sep 22, 2020 at 6:43 PM Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu> wrote: Hi James,

If freesurfer was installed under root, you should prepend sudo to the command to make changes to the directory:

sudo FREESURFER_HOME=$FREESURFER_HOME fs_install_mcr R2014b

best Andrew

From: James Hartzell <james.hartzell@gmail.commailto:james.hartzell@gmail.com> Date: Monday, September 21, 2020 at 10:49 AM To: "Hoopes, Andrew" <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu>, FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: recon-all 7.1.1

External Email - Use Caution Hi Andrew

recon-all appears to have run successfully in 7.1.1, so thanks again for all the guidance.

I've just tried to install the matlab runtime for hipp, amyg, brainstem and thalamic segmentation, as per https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime

fs_install_mcr R2014b

the command finished, but indicated a problem with. final renaming requirement: "On the target computer, append the following to your DYLD_LIBRARY_PATH environment variable: /var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84/runtime/maci64:/var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84/sys/os/maci64:/var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84/bin/maci64:

(Sep 21, 2020 16:41:29) Exiting with status 0 (Sep 21, 2020 16:41:29) End - Successful. Finished mv: rename /var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84 to /Applications/freesurfer/7.1.1/MCRv84: Permission denied

Also, if you could provide guidance for the append step, that would be great.

Cheers

James

On Sat, Sep 19, 2020 at 4:17 PM James Hartzell <james.hartzell@gmail.commailto:james.hartzell@gmail.com> wrote: Hi Andrew

Thanks for the suggestions. I removed freesurfer and reinstalled just 7.1.1. When I try to run the original patch you suggested I still get permissions problems, even with sudo.

(base) jameshartzell@Jamess-MacBook-Pro ~ % which freesurfer /Applications/freesurfer/7.1.1/bin/freesurfer

(base) jameshartzell@Jamess-MacBook-Pro freesurfer % cd $FREESURFER_HOME/bin

(base) jameshartzell@Jamess-MacBook-Pro bin % sudo mv recon-all recon-all.backup Password:

(base) jameshartzell@Jamess-MacBook-Pro bin % sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/scripts/recon... > recon-all zsh: permission denied: recon-all

Here's hoping you can send another fix!

Cheers James

-- James Hartzell, PhD (2x) Donostia-San Sebatián, Spain Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy Center for Buddhist Studies, Columbia University, USA

-- James Hartzell, PhD (2x) Donostia-San Sebatián, Spain Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy Center for Buddhist Studies, Columbia University, USA

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 http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

-- James Hartzell, PhD (2x) Donostia-San Sebatián, Spain Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy Center for Buddhist Studies, Columbia University, USA

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Hi Andrew Hope you're well and safe from Covid. I've got another problem I hope you can help with. When I open a new terminal window I see this, so something's not right, and it's causing other problems. Did I mess up my path somehow? Or is there something else I need to fix? (running Mac OS Big Sur 11.0.1 on Macbook Pro 3.3 GHz Dual-Core Intel Core i7) -------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/7.1.1 FSFAST_HOME /Applications/freesurfer/7.1.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Users/jameshartzell/freesurfer MNI_DIR /Applications/freesurfer/7.1.1/mni FSL_DIR /usr/local/fsl /etc/zshrc:7: command not found: locale /etc/zshrc_Apple_Terminal:104: command not found: mkdir (eval):116: command not found: dirname (eval):116: command not found: dirname __add_sys_prefix_to_path:6: command not found: dirname __add_sys_prefix_to_path:7: command not found: dirname touch: /Users/jameshartzell/.zsh_sessions/CCE7EE57-B042-4805-8850-D0EBEFD2F650.historynew: No such file or directory

Cheers James

On Tue, Sep 22, 2020 at 8:40 PM James Hartzell james.hartzell@gmail.com wrote:

Okay, great, thanks Andrew. I can't think of how (otherwise) I might have known not to do that! Cheers James

On Tue, Sep 22, 2020 at 8:29 PM Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:

...

Hi James, please ignore that step. In fact, adding those matlab paths to your default DYLD_LIBRARY_PATH will most likely mess up freesurfer binaries in your environment.

Andrew

*From: *James Hartzell james.hartzell@gmail.com *Date: *Tuesday, September 22, 2020 at 2:19 PM *To: *"Hoopes, Andrew" AHOOPES@mgh.harvard.edu *Cc: *FS Help freesurfer@nmr.mgh.harvard.edu *Subject: *Re: recon-all 7.1.1

•    External Email - Use Caution        *
  
  

Hi Andrew

Thanks, that works just fine.

I'll see if I can figure out how to do the path append part--just something I'm not familiar with doing:

(On the target computer, append the following to your DYLD_LIBRARY_PATH environment variable:

/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.LPxBFTBS/install-target/v84/runtime/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.LPxBFTBS/install-target/v84/sys/os/maci64:/var/folders/zz/zyxvpxvq6csfxvn_n0000000000000/T/tmp.LPxBFTBS/install-target/v84/bin/maci64:)

Cheers

James

On Tue, Sep 22, 2020 at 6:43 PM Hoopes, Andrew AHOOPES@mgh.harvard.edu wrote:

Hi James,

If freesurfer was installed under root, you should prepend sudo to the command to make changes to the directory:

sudo FREESURFER_HOME=$FREESURFER_HOME fs_install_mcr R2014b

best

Andrew

*From: *James Hartzell james.hartzell@gmail.com *Date: *Monday, September 21, 2020 at 10:49 AM *To: *"Hoopes, Andrew" AHOOPES@mgh.harvard.edu, FS Help < freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: recon-all 7.1.1

•    External Email - Use Caution        *
  
  

Hi Andrew

recon-all appears to have run successfully in 7.1.1, so thanks again for all the guidance.

I've just tried to install the matlab runtime for hipp, amyg, brainstem and thalamic segmentation,

as per

https://secure-web.cisco.com/104h7FG2WQQwJs03Se36v45YNDCtg_09GfU6HCcaeCVdgYR...

fs_install_mcr R2014b

the command finished, but indicated a problem with. final renaming requirement: "On the target computer, append the following to your DYLD_LIBRARY_PATH environment variable: /var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84/runtime/maci64:/var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84/sys/os/maci64:/var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84/bin/maci64:

(Sep 21, 2020 16:41:29) Exiting with status 0 (Sep 21, 2020 16:41:29) End - Successful. Finished mv: rename /var/folders/kl/72rg80dd57ncd7nc638fwzmh0000gn/T/tmp.0al9EPfQ/install-target/v84 to /Applications/freesurfer/7.1.1/MCRv84: Permission denied

Also, if you could provide guidance for the append step, that would be great.

Cheers

James

On Sat, Sep 19, 2020 at 4:17 PM James Hartzell james.hartzell@gmail.com wrote:

Hi Andrew

Thanks for the suggestions. I removed freesurfer and reinstalled just 7.1.1.

When I try to run the original patch you suggested I still get permissions problems, even with sudo.

(base) jameshartzell@Jamess-MacBook-Pro ~ % which freesurfer /Applications/freesurfer/7.1.1/bin/freesurfer

(base) jameshartzell@Jamess-MacBook-Pro freesurfer % cd $FREESURFER_HOME/bin

(base) jameshartzell@Jamess-MacBook-Pro bin % sudo mv recon-all recon-all.backup

Password:

(base) jameshartzell@Jamess-MacBook-Pro bin % sudo curl https://secure-web.cisco.com/1_fX_8sxYTSuMbLL5GbLODgZ0j9Apdxh-QxNTXf5dA42uFa...

...

recon-all

zsh: permission denied: recon-all

Here's hoping you can send another fix!

Cheers

James

--

James Hartzell, PhD (2x)

Donostia-San Sebatián, Spain

Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy

Center for Buddhist Studies, Columbia University, USA

--

James Hartzell, PhD (2x)

Donostia-San Sebatián, Spain

Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy

Center for Buddhist Studies, Columbia University, USA

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 http://secure-web.cisco.com/19Nt1TCVZrVU83ATlESDiM6iwNS_ohJbrc3OOILJXlORQ_w5... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

--

James Hartzell, PhD (2x)

Donostia-San Sebatián, Spain

Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy

Center for Buddhist Studies, Columbia University, USA

-- James Hartzell, PhD (2x) Donostia-San Sebatián, Spain Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy Center for Buddhist Studies, Columbia University, USA