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Miguel Ángel Rivas Fernández

16 Sep 2019 16 Sep '19

4:29 p.m.

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Dear Freesurfer devs,

I tried to open the brainmask.mgz file in freeview but I obtained this error:

mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could not open file MRIread failed: Unable to read from /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could not open file

Any suggestion about what could be the problem?, maybe the write permissons of the freesurfer folder?

I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version that is installed in a Ubuntu 18.04 virtual machine. It is very strange because few weeks ago everything it was working correctly.

Thanks in advance.

Best regards,

-- *Miguel Ángel Rivas Fernández*

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Ruopeng Wang

16 Sep 16 Sep

4:58 p.m.

If you run:

ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz

What does it show?

Ruopeng

On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote:

...

External Email - Use Caution

Dear Freesurfer devs,

I tried to open the brainmask.mgz file in freeview but I obtained this error:

mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could not open file MRIread failed: Unable to read from /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could not open file

Any suggestion about what could be the problem?, maybe the write permissons of the freesurfer folder?

I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version that is installed in a Ubuntu 18.04 virtual machine. It is very strange because few weeks ago everything it was working correctly.

Thanks in advance.

Best regards,

*Miguel Ángel Rivas Fernández*

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

Miguel Ángel Rivas Fernández

5:11 p.m.

External Email - Use Caution

Dear Ruopeng,

I put that command in the freeview command console and this is the output

[FreeView] ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz

This is not a shell. Only freeview commands are supported. Type '-h' for all the available commands.

Best regards,

El lun., 16 sept. 2019 a las 22:58, Ruopeng Wang (< rpwang@nmr.mgh.harvard.edu>) escribió:

...

If you run:

ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz

What does it show?

Ruopeng On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote:
    External Email - Use Caution
Dear Freesurfer devs,

I tried to open the brainmask.mgz file in freeview but I obtained this error:

mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could not open file MRIread failed: Unable to read from /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could not open file

Any suggestion about what could be the problem?, maybe the write permissons of the freesurfer folder?

I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version that is installed in a Ubuntu 18.04 virtual machine. It is very strange because few weeks ago everything it was working correctly.

Thanks in advance.

Best regards,

*Miguel Ángel Rivas Fernández*

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

-- *Miguel Ángel Rivas Fernández*

Ruopeng Wang

7:56 p.m.

Can you run the command in the command window that you start freeview?

Ruopeng

...

On Sep 16, 2019, at 5:11 PM, Miguel Ángel Rivas Fernández miguelrivasfdez@gmail.com wrote:
    External Email - Use Caution        
Dear Ruopeng,

I put that command in the freeview command console and this is the output

[FreeView] ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz This is not a shell. Only freeview commands are supported. Type '-h' for all the available commands.

Best regards,

El lun., 16 sept. 2019 a las 22:58, Ruopeng Wang (<rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu>) escribió: If you run:

ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz

What does it show?

Ruopeng

On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote:

...
    External Email - Use Caution        
Dear Freesurfer devs,

I tried to open the brainmask.mgz file in freeview but I obtained this error:

mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could not open file MRIread failed: Unable to read from /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could not open file

Any suggestion about what could be the problem?, maybe the write permissons of the freesurfer folder?

I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version that is installed in a Ubuntu 18.04 virtual machine. It is very strange because few weeks ago everything it was working correctly.

Thanks in advance.

Best regards,

Miguel Ángel Rivas Fernández

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

-- Miguel Ángel Rivas Fernández _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Miguel Ángel Rivas Fernández

17 Sep 17 Sep

10:22 a.m.

External Email - Use Caution

I tried in the command window where I started freeview but nothing happened. This is the output

miguel@miguel-VirtualBox:~$ ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz

El mar., 17 sept. 2019 a las 1:56, Ruopeng Wang (rpwang@nmr.mgh.harvard.edu) escribió:

...

Can you run the command in the command window that you start freeview?

Ruopeng

On Sep 16, 2019, at 5:11 PM, Miguel Ángel Rivas Fernández < miguelrivasfdez@gmail.com> wrote:
    External Email - Use Caution
Dear Ruopeng,

I put that command in the freeview command console and this is the output

[FreeView] ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz This is not a shell. Only freeview commands are supported. Type '-h' for all the available commands.

Best regards,

El lun., 16 sept. 2019 a las 22:58, Ruopeng Wang (< rpwang@nmr.mgh.harvard.edu>) escribió:

...
If you run:

ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz

What does it show?

Ruopeng On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote:
    External Email - Use Caution
Dear Freesurfer devs,

I tried to open the brainmask.mgz file in freeview but I obtained this error:

mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could not open file MRIread failed: Unable to read from /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could not open file

Any suggestion about what could be the problem?, maybe the write permissons of the freesurfer folder?

I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version that is installed in a Ubuntu 18.04 virtual machine. It is very strange because few weeks ago everything it was working correctly.

Thanks in advance.

Best regards,

*Miguel Ángel Rivas Fernández*

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- *Miguel Ángel Rivas Fernández* _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

-- *Miguel Ángel Rivas Fernández*

Ruopeng Wang

10:52 a.m.

Is your work disk full?

On 9/17/19 10:22 AM, Miguel Ángel Rivas Fernández wrote:

...

External Email - Use Caution

I tried in the command window where I started freeview but nothing happened. This is the output

miguel@miguel-VirtualBox:~$ ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz

El mar., 17 sept. 2019 a las 1:56, Ruopeng Wang (<rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu>) escribió:

Can you run the command in the command window that you start
freeview?

Ruopeng

...

On Sep 16, 2019, at 5:11 PM, Miguel Ángel Rivas Fernández
<miguelrivasfdez@gmail.com <mailto:miguelrivasfdez@gmail.com>> wrote:

        External Email - Use Caution


Dear Ruopeng,

I put that command in the freeview command console and this is
the output

[FreeView] ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
This is not a shell. Only freeview commands are supported. Type
'-h' for all the available commands.
 Best regards,

El lun., 16 sept. 2019 a las 22:58, Ruopeng Wang
(<rpwang@nmr.mgh.harvard.edu
<mailto:rpwang@nmr.mgh.harvard.edu>>) escribió:

    If you run:

    ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz

    What does it show?

    Ruopeng

    On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote:

...

            External Email - Use Caution

    Dear Freesurfer devs,

    I tried to open the brainmask.mgz file in freeview but I
    obtained this error:


    mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz,
    -1): could not open file
    MRIread failed: Unable to read from
    /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz
    mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz,
    -1): could not open file

    Any suggestion about what could be the problem?, maybe the
    write permissons of the freesurfer folder?

    I am using the
    freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
    version that is installed in a Ubuntu 18.04 virtual machine.
    It is very strange because few weeks ago everything it was
    working correctly.

    Thanks in advance.


    Best regards,
    -- 
    *Miguel Ángel Rivas Fernández*

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

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



-- 
*Miguel Ángel Rivas Fernández*
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

-- *Miguel Ángel Rivas Fernández*

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

Miguel Ángel Rivas Fernández

5:11 p.m.

External Email - Use Caution

It seems that there is enough free space in the work disk

[image: imagen.png]

El mar., 17 sept. 2019 a las 16:56, Ruopeng Wang (< rpwang@nmr.mgh.harvard.edu>) escribió:

...

Is your work disk full? On 9/17/19 10:22 AM, Miguel Ángel Rivas Fernández wrote:
    External Email - Use Caution
I tried in the command window where I started freeview but nothing happened. This is the output

miguel@miguel-VirtualBox:~$ ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz

El mar., 17 sept. 2019 a las 1:56, Ruopeng Wang (< rpwang@nmr.mgh.harvard.edu>) escribió:

...
Can you run the command in the command window that you start freeview?

Ruopeng

On Sep 16, 2019, at 5:11 PM, Miguel Ángel Rivas Fernández < miguelrivasfdez@gmail.com> wrote:
    External Email - Use Caution
Dear Ruopeng,

I put that command in the freeview command console and this is the output

[FreeView] ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz This is not a shell. Only freeview commands are supported. Type '-h' for all the available commands. Best regards,

El lun., 16 sept. 2019 a las 22:58, Ruopeng Wang (< rpwang@nmr.mgh.harvard.edu>) escribió:

...
If you run:

ls /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz

What does it show?

Ruopeng On 9/16/19 4:29 PM, Miguel Ángel Rivas Fernández wrote:
    External Email - Use Caution
Dear Freesurfer devs,

I tried to open the brainmask.mgz file in freeview but I obtained this error:

mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could not open file MRIread failed: Unable to read from /usr/local/freesurfer/subjects/4227/mri/brainmask.mgz mghRead(/usr/local/freesurfer/subjects/4227/mri/brainmask.mgz, -1): could not open file

Any suggestion about what could be the problem?, maybe the write permissons of the freesurfer folder?

I am using the freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c version that is installed in a Ubuntu 18.04 virtual machine. It is very strange because few weeks ago everything it was working correctly.

Thanks in advance.

Best regards,

*Miguel Ángel Rivas Fernández*

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- *Miguel Ángel Rivas Fernández* _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- *Miguel Ángel Rivas Fernández*

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

-- *Miguel Ángel Rivas Fernández*

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Miguel Ángel Rivas Fernández
Ruopeng Wang