Re: [Freesurfer] Passcode for 7zip archive

2022-04-29 Thread fsbuild 
External Email - Use Caution

Sending the info to your email shortly.
- R.

On Apr 29, 2022, at 07:33, Lukas Mikula mikula.lu...@mailbox.org 
wrote:External Email - Use 
CautionTo whom it may concern,I 
am in the preogress of installing Freesurfer via Virtual box and on the 
installation instruction page it says i need to send an email to the freesurf 
help mail to get the passcode to extract the FS_7_2_0_Ubuntu_18_04_06.ova.7z 
file that contains the VM image .Is this the correct emailing 
list?thank you 
sincerely,L.M___Freesurfer
 mailing 
listfreesur...@nmr..mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
___
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Re: [Freesurfer] Request for 7 zip password VM_67

2022-04-29 Thread fsbuild 
External Email - Use Caution

Sending the info to your email shortly.
- R.On Apr 28, 2022, at 16:10, Bastola, Subrat sxb2...@mavs.uta.edu 
wrote:External Email - Use 
CautionHi, I just need a 
passcode to archive the zip folder for file
FS_7_2_0_Ubuntu_18_04_06.ova.7z so that I can install free surfer virtual disk.
Regards,Subrat___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
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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
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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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 
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.