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Hi
I think i fixed it--just needed to add to PATH correctly in .zprofile
Cheers
James
On Fri, Nov 27, 2020 at 11:16 AM James Hartzell
wrote:
> Hi Andrew
> Hope you're well and safe from Covid.
> I've got another problem I hope you can help with. When
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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 someth
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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
wrote:
> Hi James, please ignore that step. In fact, adding those matlab paths to
> your defau
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
Date: Tuesday, September 22, 2020 at 2:19 PM
To: "Hoopes, Andrew"
Cc: FS Help
Subject: Re: reco
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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/
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
Date: Monday, September 21, 2020 at 10:49 AM
To: "Hoopes, Andrew" , FS Help
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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/Ma
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Hello James,
Maybe you could do a quick check to see if sudo permission is working for you.
This should always work to create and remove a file….
$ cd /tmp$ touch foo$ rm foo
… but sudo has to work for your account to do the same under /Applications
$
Did you run `chmod +x` on the re-downloaded recon-all?
Andrew
From: James Hartzell
Date: Saturday, September 19, 2020 at 11:09 AM
To: "Hoopes, Andrew"
Cc: FS Help
Subject: Re: recon-all 7.1.1
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Hi Andrew
There's still some sort of problem:
(base) jameshart
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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
$Snii.gz -au
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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
wrote:
> Hi James,
>
>
>
> Try cd`ing to yo
Hi James,
Try cd`ing to your home directory, then running:
curl
https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/scripts/recon-all
> recon-all
sudo mv recon-all $FREESURFER_HOME/bin
best
Andrew
From: James Hartzell
Date: Saturday, September 19, 2020 at 10:17 AM
To: "Hoopes, And
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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
/A
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