Re: [Freesurfer] Permission denied error from -localGI

2024-02-26 Thread Douglas N. Greve 
That is weird -- ft_read_mri is not one of our files. Can you send the 
command line and the *full* terminal output? The lGI stuff is pretty old 
and does not have a maintainer.


On 2/26/2024 1:40 PM, Michael Ruvalcaba wrote:


External Email - Use Caution

Hi Douglas,

Yes I can definitely do that!

After I run the recon -all part for a specific subject using 
freesurfer 7.2.0 in MATALB, I then run the below code:


%% 4c. Load Freesurfer Pre-Op MRI (do not edit)
addpath('/usr/local/freesurfer_x86_64-7.2.0/matlab');
fsmri_pre_acpc = ft_read_mri([subdir 
'3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']);


Which gives me the following error:

/bin/bash: 
/scratch/tp0a8d7d21_790a_4945_a04d_b0cc7d38be4f.load_mgh.m.mgh: 
Permission denied


ERROR: could not open 
/scratch/tp0a8d7d21_790a_4945_a04d_b0cc7d38be4f.load_mgh.m.mgh for reading
ERROR: loading 
/home/knight/ecog/DATA_FOLDER/UCSD/SD11/3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz 
as MGH

Dot indexing is not supported for variables of this type.

Error in ft_read_mri (line 401)
    ndims = numel(size(tmp.vol));

Error in SD11_Recon_Pipeline (line 197)
fsmri_pre_acpc = ft_read_mri([subdir 
'3D_Images/freesurfer_pre-op/freesurfer/mri/T1.mgz']);



I don't get this error when using freesurfer 6.0.0 and using those 
above commands. So I'm guessing it's because freesurfer 7.2.0 is 
trying to write something to a scratch file that doesn't even exist?


Thank you for your help!

Best,
Michael Ruvalcaba
Knight Lab
Helen Wills Neuroscience Institute
University of California, Berkeley


On Fri, Feb 23, 2024 at 10:26 AM Douglas N. Greve 
 wrote:


Can you send more info? Eg, command line, all terminal output,
version of FS you are using?

On 2/6/2024 6:18 PM, Michael Ruvalcaba wrote:


External Email - Use Caution

Hello,

I had a similar question you had in the past thread
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg72609.html

)
but I cannot seem to access the link where you solved this issue.
It looks like Tashrif helped you and he informed me to ask you

Can you help me with this by chance? I tried opening an account
and logging in but it says my account hasn't been approved yet :(
and I'm not sure who to contact to get it approved. It's been
months.

Thank you!

Best,
Michael Ruvalcaba


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Re: [Freesurfer] Permission denied error from -localGI

2022-05-16 Thread Billah, Tashrif 
Just closing this thread: we have solved it in 
https://forum.freesurfer.net/t/permission-denied-error-from-localgi/62

Thanks,
Tashrif
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Re: [Freesurfer] Permission denied error from -localGI

2022-05-02 Thread Billah, Tashrif 
No it does not exist.

-Tashrif



Douglas N. 
Greve<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=from:%22Douglas+N.+Greve%22>
 Mon, 02 May 2022 12:40:55 
-0700<https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20220502>


Does that file exist? If so what are its perms?



From: Billah, Tashrif
Sent: Friday, April 29, 2022 3:53 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Permission denied error from -localGI

Thank you Douglas. We took our time to install FreeSurfer 7.2 and retry. 
However, we ran into the same error:

>> reading filled volume...
/bin/bash: /scratch/tp7785365264536.load_mgh.m.mgh: Permission denied

ERROR: could not open /scratch/tp7785365264536.load_mgh.m.mgh for reading
ERROR: loading 
/data/pnl/FS_SUBJECTS_DIR/1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 as MGH
Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file



What can we do now?

-Tashrif


===

Douglas N. Greve Wed, 27 Apr 2022 07:51:33 -0700
Can you just try it with 7.2? We had some problems at one point with 
temporary files in lGI that were fixed with 7.2

===

On 4/27/2022 9:36 AM, Billah, Tashrif wrote:
Sorry about missing your earlier question--our FreeSurfer is 7.1.0

We still need your help with this issue.

Thank you,
Tashrif



 Douglas N. Greve Sun, 27 Mar 2022 13:57:02 -0700

===


What version of FS are you running?

On 3/20/2022 8:47 PM, Billah, Tashrif wrote:

It does not exist and cannot be created in a shared cluster.
Is there a way to define a different folder for
/scratch/tp24093955057547375.load_mgh.m.mgh?



===
Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800

Do you have permission to /scratch? Does it exist?

===
Billah, Tashrif Wed, 02 Mar 2022 06:50:41 -0800

Hi all,

We are trying to run recon-all with -localGI but running into an unknown
permission denied error:

$ recon-all -s sub-1001 -localGI

```

make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
 exit
=


< M A T L A B (R) >
Copyright 1984-2017 The MathWorks, Inc.
R2017a (9.2.0.556344) 64-bit (glnxa64)
March 27, 2017


>> reading filled volume...
/bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied


ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for 
reading

ERROR: loading
/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 as MGH
Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file
'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!


recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022

```

Our MATLAB environment is properly setup and we regularly run other
FreeSurfer-MATLAB commands. So I do not think that is causing the issue.

Best,
Tashrif
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Re: [Freesurfer] Permission denied error from -localGI

2022-05-02 Thread Douglas N. Greve 

Does that file exist? If so what are its perms?

On 4/29/2022 3:53 PM, Billah, Tashrif wrote:
Thank you Douglas. We took our time to install FreeSurfer 7.2 and 
retry. However, we ran into the same error:


>> reading filled volume...
/bin/bash: /scratch/tp7785365264536.load_mgh.m.mgh: Permission denied

ERROR: could not open /scratch/tp7785365264536.load_mgh.m.mgh for 
reading
ERROR: loading 
/data/pnl/FS_SUBJECTS_DIR/1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz 
as MGH

Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file



What can we do now?

-Tashrif


    ===
    Douglas N. Greve Wed, 27 Apr 2022 07:51:33 -0700
    Can you just try it with 7.2? We had some problems at one point 
with temporary files in lGI that were fixed with 7.2


    ===
    On 4/27/2022 9:36 AM, Billah, Tashrif wrote:
    Sorry about missing your earlier question--our FreeSurfer is 7.1.0

    We still need your help with this issue.

    Thank you,
    Tashrif



     Douglas N. Greve Sun, 27 Mar 2022 13:57:02 -0700

    ===


    What version of FS are you running?

    On 3/20/2022 8:47 PM, Billah, Tashrif wrote:

        It does not exist and cannot be created in a shared cluster.
    Is there a way to define a different folder for
    /scratch/tp24093955057547375.load_mgh.m.mgh?



    ===
    Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800

    Do you have permission to /scratch? Does it exist?

    ===
    Billah, Tashrif Wed, 02 Mar 2022 06:50:41 -0800

    Hi all,

    We are trying to run recon-all with -localGI but running into an 
unknown

    permission denied error:

    $ recon-all -s sub-1001 -localGI

    ```

make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
     exit
    =


    < M A T L A B (R) >
    Copyright 1984-2017 The MathWorks, Inc.
    R2017a (9.2.0.556344) 64-bit (glnxa64)
    March 27, 2017


    >> reading filled volume...
    /bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission 
denied



    ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh 
for reading


    ERROR: loading
/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
     as MGH
    Struct contents reference from a non-struct array object.


    Error in make_outer_surface (line 25)
    volume=vol.vol;

    >>
    ERROR: make_outer_surface did not create output file
'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!


    recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 
2022


    ```

    Our MATLAB environment is properly setup and we regularly run other
    FreeSurfer-MATLAB commands. So I do not think that is causing the 
issue.


    Best,
    Tashrif

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Re: [Freesurfer] Permission denied error from -localGI

2022-04-29 Thread Billah, Tashrif 
Thank you Douglas. We took our time to install FreeSurfer 7.2 and retry. 
However, we ran into the same error:

>> reading filled volume...
/bin/bash: /scratch/tp7785365264536.load_mgh.m.mgh: Permission denied

ERROR: could not open /scratch/tp7785365264536.load_mgh.m.mgh for reading
ERROR: loading 
/data/pnl/FS_SUBJECTS_DIR/1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 as MGH
Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file



What can we do now?

-Tashrif


===

Douglas N. Greve Wed, 27 Apr 2022 07:51:33 -0700
Can you just try it with 7.2? We had some problems at one point with 
temporary files in lGI that were fixed with 7.2

===

On 4/27/2022 9:36 AM, Billah, Tashrif wrote:
Sorry about missing your earlier question--our FreeSurfer is 7.1.0

We still need your help with this issue.

Thank you,
Tashrif



 Douglas N. Greve Sun, 27 Mar 2022 13:57:02 -0700

===


What version of FS are you running?

On 3/20/2022 8:47 PM, Billah, Tashrif wrote:

It does not exist and cannot be created in a shared cluster.
Is there a way to define a different folder for
/scratch/tp24093955057547375.load_mgh.m.mgh?



===
Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800

Do you have permission to /scratch? Does it exist?

===
Billah, Tashrif Wed, 02 Mar 2022 06:50:41 -0800

Hi all,

We are trying to run recon-all with -localGI but running into an unknown
permission denied error:

$ recon-all -s sub-1001 -localGI

```

make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
 exit
=


< M A T L A B (R) >
Copyright 1984-2017 The MathWorks, Inc.
R2017a (9.2.0.556344) 64-bit (glnxa64)
March 27, 2017


>> reading filled volume...
/bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied


ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for 
reading

ERROR: loading
/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 as MGH
Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file
'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!


recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022

```

Our MATLAB environment is properly setup and we regularly run other
FreeSurfer-MATLAB commands. So I do not think that is causing the issue.

Best,
Tashrif
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] Permission denied error from -localGI

2022-04-29 Thread Billah, Tashrif 
Thank you Douglas. We took our time to install FreeSurfer 7.2 and retry. 
However, we ran into the same error:


>> reading filled volume...
/bin/bash: /scratch/tp7785365264536.load_mgh.m.mgh: Permission denied


ERROR: could not open /scratch/tp7785365264536.load_mgh.m.mgh for reading
ERROR: loading 
/data/pnl/FS_SUBJECTS_DIR/1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 as MGH
Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file


What can we do now?

-Tashrif


Douglas N. Greve Wed, 27 Apr 2022 07:51:33 -0700

===
Can you just try it with 7.2? We had some problems at one point with temporary 
files in lGI that were fixed with 7.2

===

On 4/27/2022 9:36 AM, Billah, Tashrif wrote:
Sorry about missing your earlier question--our FreeSurfer is 7.1.0

We still need your help with this issue.

Thank you,
Tashrif



 Douglas N. Greve Sun, 27 Mar 2022 13:57:02 -0700

===


What version of FS are you running?

On 3/20/2022 8:47 PM, Billah, Tashrif wrote:

It does not exist and cannot be created in a shared cluster.
Is there a way to define a different folder for
/scratch/tp24093955057547375.load_mgh.m.mgh?



===
Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800

Do you have permission to /scratch? Does it exist?

===
Billah, Tashrif Wed, 02 Mar 2022 06:50:41 -0800

Hi all,

We are trying to run recon-all with -localGI but running into an unknown
permission denied error:

$ recon-all -s sub-1001 -localGI

```

make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
 exit
=


< M A T L A B (R) >
Copyright 1984-2017 The MathWorks, Inc.
R2017a (9.2.0.556344) 64-bit (glnxa64)
March 27, 2017


>> reading filled volume...
/bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied


ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for 
reading

ERROR: loading
/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 as MGH
Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file
'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!


recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022

```

Our MATLAB environment is properly setup and we regularly run other
FreeSurfer-MATLAB commands. So I do not think that is causing the issue.

Best,
Tashrif

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 
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 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] Permission denied error from -localGI

2022-04-27 Thread Douglas N. Greve 
Can you just try it with 7.2? We had some problems at one point with 
temporary files in lGI that were fixed with 7.2


On 4/27/2022 9:36 AM, Billah, Tashrif wrote:

Sorry about missing your earlier question--our FreeSurfer is 7.1.0

We still need your help with this issue.

Thank you,
Tashrif



     Douglas N. Greve Sun, 27 Mar 2022 13:57:02 -0700

===


What version of FS are you running?

On 3/20/2022 8:47 PM, Billah, Tashrif wrote:

    It does not exist and cannot be created in a shared cluster.
Is there a way to define a different folder for
/scratch/tp24093955057547375.load_mgh.m.mgh?



    ===
    Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800

    Do you have permission to /scratch? Does it exist?

    ===
    Billah, Tashrif Wed, 02 Mar 2022 06:50:41 -0800

    Hi all,

    We are trying to run recon-all with -localGI but running into an 
unknown

    permission denied error:

    $ recon-all -s sub-1001 -localGI

    ```

make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
     exit
    =


    < M A T L A B (R) >
    Copyright 1984-2017 The MathWorks, Inc.
    R2017a (9.2.0.556344) 64-bit (glnxa64)
    March 27, 2017


    >> reading filled volume...
    /bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission 
denied



    ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh 
for reading


    ERROR: loading
/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
     as MGH
    Struct contents reference from a non-struct array object.


    Error in make_outer_surface (line 25)
    volume=vol.vol;

    >>
    ERROR: make_outer_surface did not create output file
'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!


    recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 
2022


    ```

    Our MATLAB environment is properly setup and we regularly run other
    FreeSurfer-MATLAB commands. So I do not think that is causing the 
issue.


    Best,
    Tashrif

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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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[Freesurfer] Permission denied error from -localGI

2022-04-27 Thread Billah, Tashrif 
Sorry about missing your earlier question--our FreeSurfer is 7.1.0

We still need your help with this issue.

Thank you,
Tashrif



 Douglas N. Greve Sun, 27 Mar 2022 13:57:02 -0700

===

What version of FS are you running?

On 3/20/2022 8:47 PM, Billah, Tashrif wrote:

It does not exist and cannot be created in a shared cluster. Is there a way 
to define a different folder for /scratch/tp24093955057547375.load_mgh.m.mgh?


===
Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800

Do you have permission to /scratch? Does it exist?

===
Billah, Tashrif Wed, 02 Mar 2022 06:50:41 -0800

Hi all,

We are trying to run recon-all with -localGI but running into an unknown
permission denied error:

$ recon-all -s sub-1001 -localGI

```


make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
 exit
=


< M A T L A B (R) >
Copyright 1984-2017 The MathWorks, Inc.
R2017a (9.2.0.556344) 64-bit (glnxa64)
March 27, 2017


>> reading filled volume...
/bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied


ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for 
reading

ERROR: loading

/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 as MGH
Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file

'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!


recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022

```

Our MATLAB environment is properly setup and we regularly run other
FreeSurfer-MATLAB commands. So I do not think that is causing the issue.

Best,
Tashrif
___
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Re: [Freesurfer] Permission denied error from -localGI

2022-03-27 Thread Douglas N. Greve 

What version of FS are you running?

On 3/20/2022 8:47 PM, Billah, Tashrif wrote:
It does not exist and cannot be created in a shared cluster. Is there 
a way to define a different folder for 
/scratch/tp24093955057547375.load_mgh.m.mgh?


===
Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800

Do you have permission to /scratch? Does it exist?

===
Billah, Tashrif Wed, 02 Mar 2022 06:50:41 -0800

Hi all,

We are trying to run recon-all with -localGI but running into an unknown
permission denied error:

$ recon-all -s sub-1001 -localGI

```

make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
 exit
=


< M A T L A B (R) >
Copyright 1984-2017 The MathWorks, Inc.
R2017a (9.2.0.556344) 64-bit (glnxa64)
March 27, 2017


>> reading filled volume...
/bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied


ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for 
reading

ERROR: loading
/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 as MGH
Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file
'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!


recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022

```

Our MATLAB environment is properly setup and we regularly run other
FreeSurfer-MATLAB commands. So I do not think that is causing the issue.

Best,
Tashrif

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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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 https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] Permission denied error from -localGI

2022-03-20 Thread Billah, Tashrif 
It does not exist and cannot be created in a shared cluster. Is there a way to 
define a different folder for /scratch/tp24093955057547375.load_mgh.m.mgh?

===
Douglas N. Greve Wed, 09 Mar 2022 10:04:31 -0800

Do you have permission to /scratch? Does it exist?

===
Billah, Tashrif Wed, 02 Mar 2022 06:50:41 -0800

Hi all,

We are trying to run recon-all with -localGI but running into an unknown
permission denied error:

$ recon-all -s sub-1001 -localGI

```

make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
 exit
=


< M A T L A B (R) >
Copyright 1984-2017 The MathWorks, Inc.
R2017a (9.2.0.556344) 64-bit (glnxa64)
March 27, 2017


>> reading filled volume...
/bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied


ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for reading
ERROR: loading
/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 as MGH
Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file
'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!


recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022

```

Our MATLAB environment is properly setup and we regularly run other
FreeSurfer-MATLAB commands. So I do not think that is causing the issue.

Best,
Tashrif
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] Permission denied error from -localGI

2022-03-09 Thread Douglas N. Greve 

Do you have permission to /scratch? Does it exist?

On 3/2/2022 9:50 AM, Billah, Tashrif wrote:

Hi all,

We are trying to run recon-all with -localGI but running into an 
unknown permission denied error:


$ recon-all -s sub-1001 -localGI

```

make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); 
exit

=


< M A T L A B (R) >
Copyright 1984-2017 The MathWorks, Inc.
R2017a (9.2.0.556344) 64-bit (glnxa64)
March 27, 2017


>> reading filled volume...
/bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied


ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for 
reading
ERROR: loading 
/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz 
as MGH

Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file 
'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!



recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022

```

Our MATLAB environment is properly setup and we regularly run other 
FreeSurfer-MATLAB commands. So I do not think that is causing the issue.


Best,
Tashrif

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] Permission denied error from -localGI

2022-03-02 Thread Billah, Tashrif 
Hi all,

We are trying to run recon-all with -localGI but running into an unknown 
permission denied error:

$ recon-all -s sub-1001 -localGI

```

make_outer_surface('/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer');
 exit
=


< M A T L A B (R) >
Copyright 1984-2017 The MathWorks, Inc.
R2017a (9.2.0.556344) 64-bit (glnxa64)
March 27, 2017


>> reading filled volume...
/bin/bash: /scratch/tp24093955057547375.load_mgh.m.mgh: Permission denied


ERROR: could not open /scratch/tp24093955057547375.load_mgh.m.mgh for reading
ERROR: loading 
/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 as MGH
Struct contents reference from a non-struct array object.


Error in make_outer_surface (line 25)
volume=vol.vol;

>>
ERROR: make_outer_surface did not create output file 
'/path/to/FS_SUBJECTS_DIR/sub-1001/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'!


recon-all -s sub-1001 exited with ERRORS at Wed Mar 2 09:02:21 EST 2022

```

Our MATLAB environment is properly setup and we regularly run other 
FreeSurfer-MATLAB commands. So I do not think that is causing the issue.

Best,
Tashrif
___
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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 .
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