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Hi Hui,

Ok, we've found the problem - the downloaded file (miniconda_installer.sh) is actually empty, so the download is failing.

What happens when you run this command instead (i.e. passing -L  to curl ?

curl -o miniconda_installer.sh -L --fail https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
echo $?
md5 miniconda_installer.sh

If this works, you should be able to fix the FSL installation like so:

1. Open the fslpython_install.sh script in a text editor (you may need to use sudo)
2. Find line 149 - its contents should be:
       dl_cmd_opts="--fail"
3. Change this line to:
      dl_cmd_opts="--fail -L"
4. Repeat these two commands:
           sudo rm -r /usr/local/fsl/fslpython
    sudo /usr/local/fsl/etc/fslconf/fslpython_install.sh  -f  /usr/local/fsl


Thanks for your patience through all of this,

Paul

On Apr 9 2020, at 12:06 pm, Hui Xu <[log in to unmask]> wrote:
Hi Paul,

I have tried the following commands, and what have been reported as following:

curl -o miniconda_installer.sh --fail https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
       % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current  Dload  Upload   Total   Spent    Left  Speed


        0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0



echo $? 
        0

md5 miniconda_installer.sh
   MD5 (miniconda_installer.sh) = d41d8cd98f00b204e9800998ecf8427e

The internet connection is reliable and fast in my office.

Best,
Hui


在 2020-04-09 17:55:55，"paul mccarthy" <[log in to unmask]> 写道：

Hi Hui,

Well to me this looks like it could simply be an unreliable internet connection. The FSL installation needs a reliable and fast internet connection to complete successfully.

What happens when you run these commands?

curl -o miniconda_installer.sh --fail https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh
       % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current


                                 Dload  Upload   Total   Spent    Left  Speed

        0     0    0     0    0     0      0      0 --:--:--  0:00:02 --:--:--     0

echo $? 
        0
md5 miniconda_installer.sh
   MD5 (miniconda_installer.sh) = d41d8cd98f00b204e9800998ecf8427e


Paul

On Apr 9 2020, at 1:47 am, Hui Xu <[log in to unmask]> wrote:
Hi Paul,

The following content was seen in the fslpython_miniconda_installer.log  file:

Installing FSL conda distribution into /usr/local/fsl/fslpython
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:03 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:03 --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:03 --:--:--     0
/usr/local/fsl/etc/fslconf/fslpython_install.sh: line 203: /usr/local/fsl/fslpython/bin/conda: No such file or directory

I have tried "sudo /bin/bash /usr/local/fsl/etc/fslconf/fslpython_install.sh  -f  /usr/local/fsl", unlucky, the same error happened.

Thanks a lot.

Hui



在 2020-04-09 00:25:36，"paul mccarthy" <[log in to unmask]> 写道：

Hi Karolina and Hui,

And is there any output at all in the fslpython_miniconda_installer.log  file that is mentioned?

I'm not entirely sure what is going wrong - it could be that the miniconda installer script is somehow not compatible with zsh  (the default shell in macOS catalina). You could try running the installation from bash:

sudo /bin/bash /usr/local/fsl/etc/fslconf/fslpython_install.sh  -f  /usr/local/fsl

Although I have no idea if this will work, as I don't have access to a mac, and cannot reproduce the problem.

Paul

On Apr 8 2020, at 3:20 pm, Hui Xu <[log in to unmask]> wrote:
Hi Paul,

Really appreciate your help. The exact commands I executed were as following:

rm -r /usr/local/fsl/fslpython
sudo /usr/local/fsl/etc/fslconf/fslpython_install.sh  -f  /usr/local/fsl

Then detailed information reported as following:
Stage 1
By installing this python distribution you agree to the license terms in
/usr/local/fsl/fslpython/LICENSE.txt
100%
/usr/local/fsl/etc/fslconf/fslpython_install.sh: line 188: /usr/local/fsl/fslpython/bin/conda: No such file or directory
/usr/local/fsl/etc/fslconf/fslpython_install.sh: line 189: /usr/local/fsl/fslpython/bin/conda: No such file or directory
/usr/local/fsl/etc/fslconf/fslpython_install.sh: line 190: /usr/local/fsl/fslpython/bin/conda: No such file or directory
/usr/local/fsl/etc/fslconf/fslpython_install.sh: line 191: /usr/local/fsl/fslpython/bin/conda: No such file or directory
Stage 2
100%
Failed to create FSL Python environment - see /var/folders/1m/_gr08pjj797b115ckgq8v0fc0000gn/T/fslpythonXXXX.9ODBwQF8/fslpython_miniconda_installer.log for details

Today, I also tried to re-install the fsl to check whether fsleyes could work. After downloading the fsl packages, the same above error reported. Finally, fsleyes wasn't installed.

The computer system which I worked on is macOS Catalina 10.15.4.

Best,
Hui






At 2020-04-08 17:47:49, "paul mccarthy" <[log in to unmask]> wrote:

Hi Hui,

Could you give more details? Please give the exact commands that you executed, and the full output of each of them.

Paul

On Apr 8 2020, at 2:14 am, Hui Xu <[log in to unmask]> wrote:
Hi Paul,

I have done as what you recommended. But this following errors reported:
/usr/local/fsl/fslpython/bin/conda: No such file or directory
Failed to create FSL Python environment - see /var/folders/gy/kql2mkv97lx3yt7_l_xxwq840000gn/T/fslpythonXXXX.kXxwR2Tv/fslpython_miniconda_installer.log for details

I have checked the log, nothing.

Best,
Hui
在 2020-04-07 16:03:37，"paul mccarthy" <[log in to unmask]> 写道：

Hi Hui and Gabriel,

If FSLeyes is missing, then this suggests that the installation did not complete successfully.

Could you type imcp  into a terminal? If imcp  is also missing, then the installation definitely failed.

You can re-run this stage of the installation by following these steps (assuming you installed FSL into /usr/local/fsl/):

1) Deleting the folder /usr/local/fsl/fslpython
2) Reinstall fslpython with
    /usr/local/fsl/etc/fslconf/fslpython_install.sh -f /ust/local/fsl

Note you may need to run the above command with sudo, depending on your account’s privileges.

Paul
On Apr 7 2020, at 5:13 am, Hui Xu <[log in to unmask]> wrote:
Cool! The same as me, and my computer system is MacOS Catalina. I deeply regret that I have updated the computer system.

 I will try to solve this problem as you mentioned.

Thank you very much.

Best,
Hui





At 2020-04-07 12:07:35, "Gabriel Ram írez García" <[log in to unmask]> wrote:
>I experienced same problem when I installed FSL in my computer MacOS Catalina. 
>
>Installation happened without any error, but fsleyes wasn't installed. I reinstalled fsl but the problem remainded. So, I moved fsleyes app and the executable from another Mac computer to this one to added them in the proper path. This acction solved the problem. 
>
>You could try it if you have another computer with the same operating system.
>
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