Re: [Freesurfer] Failing to execute QDEC

2023-02-24 Thread fsbuild 
External Email - Use Caution

Hello Vittal,
Just FYI, the qdec program is deprecated in 7.X releases and is no longer 
maintained. In the 7.X releases, you can try using freeview for images 
and from the command line there are the mri* commands (mris_surf2surf, 
mri_glmfit, mri_glmfit-sim, etc.) for stream processing.
The license files from older versions of freesrufer, e.g., version 6, are not 
guaranteed to work on newer versions of linux OS’s because of changes to the 
crypt libraries. But a new license should work with a 7.X release.
Please in the future do not post any license files or content from them to the 
public mailing list. We can instruct you how to otherwise upload files 
for us to view.
- R.
On Feb 24, 2023, at 12:15, Wighton, Paul pwigh...@mgh.harvard.edu 
wrote:Hi Vittal,I tested your license file and it's fine. Are you sure 
it's in the right place? What's the output of `cat 
/usr/local/freesurfer/license.txt`?It also looks like QDEC is trying to write 
to `/usr/local/freesurfer/subjects/qdec/Untitled/contrasts.sig.mgh` do you have 
permissions to write there? I'd suggest creating a FreeSurfer subjects 
directory under your home and setting the SUBJECTS_DIR environment variable 
accordingly, e.g.mkdir ~/fs-subjectsexport 
SUBJECTS_DIR="${HOME}/fs-subjects"-PaulFrom:
 freesurfer-boun...@nmr.mgh.harvard.edu 
freesurfer-boun...@nmr.mgh.harvard.edu on behalf of vittal korann 
vittalkor...@gmail.comSent: Friday, February 24, 2023 11:56 AMTo: 
Freesurfer support listSubject: Re: [Freesurfer] Failing to execute 
QDECExternal Email - Use CautionHi 
Freesurfer experts,I am looking forward to resolve this issue.Any help would be 
greatly appreciated!With regards,VittalOn Wed, Feb 22, 2023 at 3:13 PM vittal 
korann vittalkor...@gmail.commailto:vittalkor...@gmail.com; 
wrote:Hi Freesurfer experts,I am trying to run Qdec on schizophrenia pre and 
post intervention scans.I created .dat and .levels files within the qdec 
folders and loaded the .dat file into qdec gui.It is suddenly crashing when I 
select my design and hit the Analyze button.And the same error message copied 
below from the terminal.Writing to 
/usr/local/freesurfer/subjects/qdec/Untitled/contrasts.sig.mgh--ERROR:
 Invalid FreeSurfer license key found in license file 
/usr/local/freesurfer/license.txtIf you are outside the NMR-Martinos 
Center,go to MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://secure-web.cisco.com/1nLzKBZWbv5Bmrf0Y03boA8pp7LUIugSlf4PhO_BVoRF79seW6OcSjoIwT97WON1wW_MzEwIItT2i78jmHwQIvK9KqWizQxU_lYkxIKx3sOHCzWvpA1Oyi53WJlHEqKhoUR5D3v7zc8zQVqyFIfegOHeRMpzjPyR53-RmmpomSEfMa_7Ll3myC5xtMM9g9k4Di1Y32rkrh97csBOeZcd2Dd24ALJ8s6yu_qMZF617WXj-_IvUJMvhKEhizUtjEPE08vzV8fH3pn1vDDEkuKCjdEgloizkGHMN5KWdvQsg3gwyBevfdapGlzRLiZbBNOdZ/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%26lt;http://secure-web.cisco.com/1uhHCIAivVgEW5Bm1C6V4wiOl6PpIl1vQPQwioRo0ISy7gTvmYGRiROjYvWNLIXP4TtQ-5sG7me0I1sCSqD-KDIHQCubfD6puAoIGdTVWRhkhxv6VU95sg_g_tTHIyfErQMIT7ZwXqVBkWyEFqVc6Bcqu111xCzBA3goA4Z9jX_VUNRjfypbFPpeLWe_6o5BzNg2utZJ_4-I4416ZHp5JZdrtv6rw-mpXRuOZJoSZKjmvFJ-XCpc7ngf0VZqJjezsNzwE-vzhDTK6mEoVbbHdnL8E2-M7n3jRreMhtc0XpTAMKGj7blsedGj2hZ3G3ob_71kTFSJq7oCcn0ddBBMWBA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu;
 toget a valid license file (it's free).If you are inside the 
NMR-Martinos Center,make sure to source the standard environment.Even 
though I renewed my license file, the issue still persists.FYI I did use qdec 
in the past and am quite comfortable with it.Also, I attached my license file 
if anything is missing.Any help would be appreciated!With 
regardsVittal___Freesurfer mailing 
listfreesur...@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
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.

Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic segmentation

2023-02-24 Thread Kumar, Avnish 
Hi Aaron,

This patch fixes a bug in the core.py file on FS-v7.3.2. In the file, one of 
the arguments for the image.resize() function call was accidentally named 
'interp'.
 The correct argument name is 
'method'.

This fix shouldn't affect the standard recon-all results.

Best,
Avnish


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Aaron Tanenbaum 

Sent: Thursday, February 23, 2023 9:12 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic 
segmentation


External Email - Use Caution

Hi,
I saw this thread and was wondering about the details of this patch. Does this 
patch affect the standard recon-all call or is this meant for a special flag. 
Also I was also wondering what issue did it solve?
Thank you.

On Wed, Feb 22, 2023 at 11:52 PM Kumar, Avnish 
mailto:avnish.ku...@mgh.harvard.edu>> wrote:
Hi Katie,

The core.py file has been updated now. Please try downloading it again and 
applying the same 
fix
 as before.

Best,
Avnish

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Katie Rose Jobson 
mailto:katie.job...@temple.edu>>
Sent: Monday, February 6, 2023 3:17 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic 
segmentation


External Email - Use Caution

Hi FS experts,

Apologies for my late follow up.

In reference to the previous conversation, I added the core.py file to the 
correct subdirectory to complete the thalamic nuclei segmentation. I received 
an error still, albeit a different error:


Traceback (most recent call last):

  File "/usr/local/freesurfer-7.3.2/python/scripts/segment_subregions", line 6, 
in 

from freesurfer import subregions

  File 
"/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/__init__.py",
 line 1, in 

from freesurfer.subregions.process import structure_names

  File 
"/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/process.py", 
line 8, in 

from freesurfer.subregions.thalamus import ThalamicNuclei

  File 
"/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/thalamus.py",
 line 9, in 

from freesurfer.subregions.core import MeshModel

  File 
"/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/core.py", 
line 9, in 

from gems.subregions import utils

ImportError: cannot import name 'utils' from 'gems.subregions' (unknown 
location)

I am assuming this is because the core.py script was previously housed in the 
'/gems/subregions' subdirectory, and is attempting to import 'utils' from 
there. Is there any way to edit this file (core.py) to call on this 'utils' 
function?

Please let me know if I can clarify my question in any way and thank you in 
advance for your help!

Best Wishes,
Katie
--
Katie Jobson, M.S. | Personal 
Website
Ph.D. Student | Cognitive Neuroscience 
Lab
Department of Psychology and Neuroscience | Temple University


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Kumar, Avnish 
mailto:avnish.ku...@mgh.harvard.edu>>
Sent: Thursday, December 8, 2022 10:19 AM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [External] Re: [Freesurfer]

Re: [Freesurfer] Failing to execute QDEC

2023-02-24 Thread Wighton, Paul 
Hi Vittal,

I tested your license file and it's fine.  Are you sure it's in the right 
place?  What's the output of `cat /usr/local/freesurfer/license.txt`?

It also looks like QDEC is trying to write to 
`/usr/local/freesurfer/subjects/qdec/Untitled/contrasts.sig.mgh` do you have 
permissions to write there?  I'd suggest creating a FreeSurfer subjects 
directory under your home and setting the SUBJECTS_DIR environment variable 
accordingly, e.g.

mkdir ~/fs-subjects
export SUBJECTS_DIR="${HOME}/fs-subjects"

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of vittal korann 

Sent: Friday, February 24, 2023 11:56 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Failing to execute QDEC

External Email - Use Caution

Hi Freesurfer experts,

I am looking forward to resolve this issue.
Any help would be greatly appreciated!

With regards,
Vittal



On Wed, Feb 22, 2023 at 3:13 PM vittal korann 
mailto:vittalkor...@gmail.com>> wrote:
Hi Freesurfer experts,

I am trying to run Qdec on schizophrenia pre and post intervention scans.
I created .dat and .levels  files within the qdec folders and loaded the .dat 
file into qdec gui.
It is suddenly crashing when I select my design and hit the Analyze button.
And the same error message copied below from the terminal.

 Writing to /usr/local/freesurfer/subjects/qdec/Untitled/contrasts.sig.mgh
--
ERROR: Invalid FreeSurfer license key found in license file 
/usr/local/freesurfer/license.txt
  If you are outside the NMR-Martinos Center,
  go to MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://surfer.nmr.mgh.harvard.edu
 to
  get a valid license file (it's free).
  If you are inside the NMR-Martinos Center,
  make sure to source the standard environment.

Even though I renewed my license file, the issue still persists.
FYI I did use qdec in the past and am quite comfortable with it.
Also, I attached my license file if anything is missing.

Any help would be appreciated!

With regards
Vittal


___
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.

Re: [Freesurfer] Failing to execute QDEC

2023-02-24 Thread vittal korann 
External Email - Use Caution

Hi Freesurfer experts,

I am looking forward to resolve this issue.
Any help would be greatly appreciated!

With regards,
Vittal



On Wed, Feb 22, 2023 at 3:13 PM vittal korann 
wrote:

> Hi Freesurfer experts,
>
> I am trying to run Qdec on schizophrenia pre and post intervention scans.
> I created .dat and .levels  files within the qdec folders and loaded the
> .dat file into qdec gui.
> It is suddenly crashing when I select my design and hit the Analyze button.
> And the same error message copied below from the terminal.
>
>  Writing to /usr/local/freesurfer/subjects/qdec/Untitled/contrasts.sig.mgh
> --
> ERROR: Invalid FreeSurfer license key found in license file
> /usr/local/freesurfer/license.txt
>   If you are outside the NMR-Martinos Center,
>   go to 
> http://secure-web.cisco.com/1uhHCIAivVgEW5Bm1C6V4wiOl6PpIl1vQPQwioRo0ISy7gTvmYGRiROjYvWNLIXP4TtQ-5sG7me0I1sCSqD-KDIHQCubfD6puAoIGdTVWRhkhxv6VU95sg_g_tTHIyfErQMIT7ZwXqVBkWyEFqVc6Bcqu111xCzBA3goA4Z9jX_VUNRjfypbFPpeLWe_6o5BzNg2utZJ_4-I4416ZHp5JZdrtv6rw-mpXRuOZJoSZKjmvFJ-XCpc7ngf0VZqJjezsNzwE-vzhDTK6mEoVbbHdnL8E2-M7n3jRreMhtc0XpTAMKGj7blsedGj2hZ3G3ob_71kTFSJq7oCcn0ddBBMWBA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu
>  to
>   get a valid license file (it's free).
>   If you are inside the NMR-Martinos Center,
>   make sure to source the standard environment.
>
> Even though I renewed my license file, the issue still persists.
> FYI I did use qdec in the past and am quite comfortable with it.
> Also, I attached my license file if anything is missing.
>
> Any help would be appreciated!
>
> With regards
> Vittal
>
>
___
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.

Re: [Freesurfer] FreeSurfer installation in a Code Ocean Capsule

2023-02-24 Thread fsbuild 
External Email - Use Caution

Hello Chiara,
It reads like Code Ocean wants to be a solution for someone to host all their 
research files for published articles, scripts, applications and binaries to 
run - in 1 place. But it’s not clear to me applications/scripts/binaries 
can be run from there in real-time. It looks more like another form of 
source control, e.g., GitHub, to enable sharing and managing of files 
(including disaster recovery).
The text at the bottom of this 
page,https://secure-web.cisco.com/1aH9sOdWmoRBiry1WokL4RYzdttBbVqc-sCSp1N3OC-uGLT2qBkRJd6vqH3_fkvCX_A6IeReQhXDV2cEVEr8ToFCntucsRr9gnDHMjk384H_-Q_EtelHBLQvoNGEV0WPb5rRrd9IqfgBgJyLZi0pH3R-ncw7k8M7mOXyOL8657_-_pCi1IEhefF7NrFSR_d93m2l4rKYKtFtU6dXKc0MtGYoCugqOX-pSzYoz24rLAFyzERSTWodnQt-htayc5ONZeb0pfKf4McsLEspxf_0qsMwt3eAH97IzcXfdIjz1VHQl2qNzsKsfhY6cyPIxReOYVmTz7XDrqf0p9Lrte0wnQg/https%3A%2F%2Fcodeocean.com%2Fproduct%2F,
 indicates they use Amazon AWS servers. So maybe a code capsule would 
connect with and run software via an AWS server image with the needed software 
installed. That server would in turn need to run a flavor of linux that 
would allow installing one of the freesurfer distribution packages 
fromhttps://secure-web.cisco.com/17phn5CctlPx0-cSxitH_2EOSCGyEjytacc8qy9k2RLxkApD7ge8Mfi1dpgW1O7dZgG-LaWUrc0zEs9aYC2Zz8jxtqJ6ZTqzlIMnhTUtk0omBjE0fW25UJRiG_PwLSjRu4nmH9X-7mIdnQ5j4CO_nmimb9ihj58KPkUrDS5uWrl7rQ4-5EVj7uxWvz1zOA2oIq_L1g3Zo1IeMpbu4WSuxVvzTONuQuAhstcnoVUDC7wPhyL8dLY8lt0YqPlrvKUzAH9NugLd919ikUCmtw7LEpw46to5_b19MSdho4fgFoMwKGe62RRZlOUFgCjootxbF63hdmd6-9gajYEqeBHWZMQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frel7downloads
For scientific clusters, you usually file a ticket to request installation of a 
software package not already available to run on the cluster. I would ask 
Code Ocean tech support how a code capsule currently runs python scripts and/or 
linux binaries in real-time from a users account. If that already works 
to run python scripts or some programs installed on linux servers, then you 
could ask tech support how 3rd party software packages (like freesurfer) could 
be managed and installed to run from a users account.
- R.

On Feb 24, 2023, at 03:50, Chiara Marzi - UniFI chiara.ma...@unifi.it 
wrote:External Email - Use 
CautionDear Freesurfer,
I am trying to use some FreeSurfer tools inside a Code Ocean capsule 
(MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to 
behttps://secure-web.cisco.com/1-WWfxxHb5KgsxJyNmbX2M5iZmuUeIU8z2QsbWvYbriKD4AiU_FiRgf_eKbJMPcvo_KHOjz9fkbjdakm3l1Owhy7wMf57UYVKMTewVwC5tACzxW5VnE92lZnHtBGaRkXJqAfzC0s99373tnftyarXoU6SIWCnq_ffvXgBSfdqXMrYtZARIsfWPz6W5Cp2PQRYOhokfl0BwjpaPref7xCvH980up8AIHjgQLTfZa7Y5ZL9K-SMJasb64jB5ss9i_dN-_pSHNm0CIjI6TveSPzGK7mQBJvfU5bk73lnEm7OJ4I9ICHDRrJ6oURs_oma-WhU9Z0pTx36r6pE731zrTGb_g/https%3A%2F%2Fcodeocean.com%2F),a
 cloud-based computational reproducibility platform that provides researchers 
and developers an easy way to share, discover, and run code published in 
academic journals and conferences.Specifically, I set up my capsule 
environment including a Python package (freely available at Github: XXX) that 
requires FreeSurfer for full functionality. Is it possible to install 
FreeSurfer on such a platform? Do you have any suggestions?Thanks!Have a nice 
day,Chiara___Freesurfer mailing 
listfreesur...@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
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] FreeSurfer installation in a Code Ocean Capsule

2023-02-24 Thread Chiara Marzi - UniFI 
External Email - Use Caution

Dear Freesurfer,

I am trying to use some FreeSurfer tools inside a Code Ocean capsule 
(https://secure-web.cisco.com/1F1n6n0E7KQZBogoJ-y7cciJe_z3d-WxxhEPHp2zwkasImEBZvKePlK6P71av7i50AM4Z0TPRLdriPQ7fWxL-OnFfVOJBHQItgkdxdjByqeRfMyJTCMrcEaYvsJALn5lt0BoJz9mhOnZov_LnVy8BA9UxVAXV9lPIp95DeliRnEb7EglpOU15Cr01bkzW-Ujv_8-zio2c4flgN5rCGeA5OvdySKaFfr5FqLTVxhbh2XdyazQPvbl659YegRcnM3r5hRW7YC3DI5LZ8SglrZ_BCNJxxDeSphOLIyb5Gp3p9dwI4HC8JjcVZ50qJtXwEr5WYGcmnTNER5j7w-2CdJB9gA/https%3A%2F%2Fcodeocean.com%2F),
 a cloud-based computational reproducibility platform that provides researchers 
and developers an easy way to share, discover, and run code published in 
academic journals and conferences. 

Specifically, I set up my capsule environment including a Python package 
(freely available at Github: XXX) that requires FreeSurfer for full 
functionality. Is it possible to install FreeSurfer on such a platform? Do you 
have any suggestions?

Thanks!

Have a nice day,
Chiara___
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.