[Freesurfer] FreeSurfer error when running Hippocampal Subfields

2021-05-14 Thread Joana Collet i Fàbregas 
External Email - Use Caution

Good morning,

I am a Biomedical Engineering Student at Universitat de Barcelona and I am
creating a python script that has a Watchdog which detects new patients in
a specific folder, and we want it to run FS and Hippocampal Subfields. The
FS runs properly, but when the script arrives to the Hippocampal Subfields
command, it breaks.

When using the FreeSurfer's Hippocampal Subfields from a python script
after running FS recon-all right before, the processing is not performed
due to the error shown in the attatched file. However, when running the
Hippocampal Subfields from the terminal it does work.

We have even tried to create a watchdog only for the Hippocampal Subfields,
and when we move a folder obtained after running FS to a specific folder,
it also runs properly. It is only when it is concatenated with FS that it
does not work.

We have contacted MathWorks Support, but they told us to reach you. The
Matlab versions we have are Matlab_R2020a and Matlab_R2014b.

Thanks a lot,

Joana Collet


hippocampal-subfields-T1 (1).log
Description: Binary data


matlab_crash_dump.26817-2 - Jupyter Text Editor (1).pdf
Description: Adobe PDF document
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Cerebellum Segementation

2021-05-14 Thread A.R. Sekar 
External Email - Use Caution

Hello Experts!

This is the first time I am doing tractography and my aim is to do it 
specifically for the cerebellum. I saw online that FreeSurfurer can segment the 
cerebellum, to create the ROI but I’m not entirely sure how to go about this. 
So far I have done the pre-processing, co-registration onto diffusion space and 
created FOD. It would be great if you could give me advice and any feedback 
about the pipeline.

Thanks for your help!

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

Re: [Freesurfer] how to visualize statistical maps in FS7.1?

2021-05-14 Thread Bernardoni, Fabio 
External Email - Use Caution

Dear Greve,

thanks for your reply.
These are my steps (I corrected the second):

1) I open the inflated surface:

tksurferfv fsaverage lh inflated

(this successfully displays the inflated left hemisphere of the average subject)

2) I now load the overlay from the freeview window (sig.mgh from a mri_glmfit)

(this successfully overlays the -log(p) statistical map)

3) I would like to threshold the map using FDR<.05. This was possible in 
tksurfer:
https://secure-web.cisco.com/1Zl2C3ogXmhGUNaxqBtskesqKl5yJdBXWaIvAlRRQc78fBLhpOj_v_7pLy07rK0_Z6hz1XHxScIJY7gHTDUT17eiC8QX-MPYtvtt7GifemJKKPlDazCGKddv42OFS-Gwz2Z4fU12mu5IIXu1ZOINcKdasomLeTOTciS1_66TzuhEVpsJO_1cUjEVdrvmJkzs2aUNzN0GI8TZP6AofozZwh9xw1gvOcAB0tP8q-6-w-u5zc27Rt1QOJOHmkIRN9l_0g_L8DOdhDNfRUbn10u7wCA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTkSurferGuide%2FTkSurferWorkingWithData%2FTkSurferOverlay

however no such option appears in tksurferfv / freeview

Any hint at this point?

Thanks a lot

Fabio


Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/1YX3ipy7sscoJinbT24JROYpvfMLxUzj6WI8zTOix4cybxxCpuT0Pg_pkoLQLv7n5vAYqezvCBlC0IVATrRHdYuJ4tGGbBP7iHyIc4b54qDva92Ito4SGjZegyEvhQIz36JtilEpoZH3vbMxrYF7RZgMx_7wHkkbBj9oa41Mdk6eNPRh4TodNL1Ro8ltljQMkYFuQ-9cCs54cHXYkwpVkamTIweEnN3l7k_zjj6kQfkcl9ii4GSg485eIYx-5mpZD2Wyn3xmDyLYAGv_j9iyyyA/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/1FLummlkSSdFqIQV8zg9pbFpjFgeXVHEbYHk2pa_UduhDt_bSjIPmILuhE9ffjkaYKrDBtYwuMXxg35s-lBplbWKOdhWKO6jW2yQlWTIDnZd48dpf70OWhl07hTefqn68qJ4v8ExrpOtfQhvav0_NHwz1W290JJfYWpXsuayJRZutZqcukbatksxvIABLFv-Ic6zLF06gmCN3ABzCcXsGPlhgvtslwReMK-welB7knanannNBYCEnsNHgvLC57qCTUNZq75tGHtQFFq4G8dX4KQ/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://secure-web.cisco.com/14YWF1gwph2SJoLo23bw_XI_Fbt7k9lApqP-e0tKnEcSkhso74cT7TR0_W-2NU7zviguEOJNHbtwedhBxO4muoLSq4FlJ1SCdu057ZeaVsPfdc-gwZFcrm8fOgx00KR_ZyTgCmDaQymWKy7evJq1mY6I0NQ92ifbpMQW5MgiefhdwmaH9x_CSaoDAuFaEH6gWZmJMZsh-syBOBXW1aMR1YGOixzHN_0P94VWN-t7JJalg0SL0O01n7IEQkYOBBWKTtvJe5g9sErSKYHN-UrDrhA/http%3A%2F%2Fwww.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/14YWF1gwph2SJoLo23bw_XI_Fbt7k9lApqP-e0tKnEcSkhso74cT7TR0_W-2NU7zviguEOJNHbtwedhBxO4muoLSq4FlJ1SCdu057ZeaVsPfdc-gwZFcrm8fOgx00KR_ZyTgCmDaQymWKy7evJq1mY6I0NQ92ifbpMQW5MgiefhdwmaH9x_CSaoDAuFaEH6gWZmJMZsh-syBOBXW1aMR1YGOixzHN_0P94VWN-t7JJalg0SL0O01n7IEQkYOBBWKTtvJe5g9sErSKYHN-UrDrhA/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113


Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Douglas N. Greve 

Gesendet: Donnerstag, 13. Mai 2021 17:11:29
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] how to visualize statistical maps in FS7.1?

your tksurferfv command line is wrong

On 5/12/2021 6:06 AM, Bernardoni, Fabio wrote:
>  External Email - Use Caution
>
> Dear Freesurfers
>
> I recently moved to FS7.1 and I was trying to reproduce my workflow I had 
> with FS5.3.
>
> To visualize statistical maps, I had always used tksurfer. It seems, however, 
> it is no longer maintained.
>
> When I launch it it fails to find out the tix, tcl, etc libraries. Following 
> this thread:
> https://secure-web.cisco.com/1v7sQGKZgCQ9d6BT0fUpIf9QvmP5selhkoGYWs1-X9TSsF6ebf9WkfXQKwNGkJnbQTNihRlUwkt3d_MtgGepc7G9MM_ZkCKisZX1hKBJ9twis_mX1rWvKXW84_u67FO-1Nf-Nw0XV4e4TaksCUTJbLoVykRInrujR5kv4RuP668hB4uZuRSUTzw5Wv0cdJpuX2G2CxoXrNGsfZPGI9wEQy2xuY0fWpzXbjw3A6IN30dlVGcFiz2RxbN4DmxS9mgJACyaWUAW4XrSh_mrEyukmaw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg66219.html
>
> I tried to use tksurferfv.  However, when trying to overlay the sig.mgh 
> output of mriglmfit, on an inflated fsaverage surface, the program shuts 
> down, with this error:
>
> freeview -f 
> /usr/local/freesurfer/subjects/fsaverage/surf/lh.inflated:curvature=/usr/local/freesurfer/subjects/fsaverage/surf/lh.curv
>  -viewport 3d
> terminate called after throwing an instance of 'int'
> Abort (core dumped)
>
>
>
>
>
> What would you suggest to visualize statistical maps in FS7? Is my problem 
> expected?
>
> Thank you in advance for your attention
>
> Fabio
>
>
> Dr. Fabio Bernardoni
> wiss. Mitarbeiter
>
> Division of Psychological & Social Medicine and Developmental Neurosciences
> http://secure-web.cisco.com/1fJ-kcGEyM5xIf9EYKEBdxq9jOYgp4LWrcrsRqW2VW0t2XhEyJg3GuHzjb7IPAU-FCiyn7epXi34kENaICaL_b

Re: [Freesurfer] how to visualize statistical maps in FS7.1?

2021-05-14 Thread Bernardoni, Fabio 
External Email - Use Caution

Ok I found a solution using separately mri_fdr

thanks anyway!

Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/15vnpAEjrPYiKn6yEt0jIUfHx8_4Erx_TvQU05r-dRGFvX5o0_mKiLNQoOoY_DiUFEu3Zb0adehInmHSUaelrON7US4wQ_sWBoQxe2WEPWflAevksiDhq9xUM0HpqhFyVYQ_E6lAcMbhVCVy7BrdLpkrKVNjZklIfxcHcWr5x_R8nAnO3kseYCYgupaYK0YfQU5rXE3-xyfRoCRuDtLtXKnJmnAG9REL9uq0BV_7ZXuM239yt3PhScBv-jdmCWqnVKhzsluD3IrIBTh6UsOy7mQ/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/1PoiqfrNJCTGfMCCkQlttMgDYdjJ_kf3kZ8cHx_f-PnnR1ou9CYrXL4wwpARdd5jBIoEyyH6WRwiGcI2zF0MEzpoexufmjhvKmf_TJMFBg6Cielu-V9qKgk7jDZWTcDm2ciqEtHGLSlLLw-eqLWYalhfAFef1y44MmoHa3utLtAl3loyhlAUlPlAjROXw1deJfxT8nmYTPE19cdW9XGZWokm5kWZ2Nqc_Stox4LWVgzrO1P3Dxj11oUM0MCPkWo0tV7otPW3zFFqjc20pMEyZRA/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://secure-web.cisco.com/1riQaRreNdNrwHCBcJyC31n1f-pTKoB2pPlPL__pKwfPnlE9wTZTAJNlsiJ6CXVC8apuYz6dFGIc1aVTnHi5W3mdfNBjvE7ZAMaz9J6CkDXsrjZAqn-5yiTvOMfa7hWBAzLaL9DLq96R-OfWXlCoeXb581P16Xlk1SQTkboYrxiV5NN9-Rm6X0gTwGR6a-Hle8XLEhHWkemWuP14oQh3hUYcKd-Jy2i83tVqPsJHT3uc9kPdhknHTLJ6W6sivC7thhbiy-xNhsiGRO3g2L3Eujw/http%3A%2F%2Fwww.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/1riQaRreNdNrwHCBcJyC31n1f-pTKoB2pPlPL__pKwfPnlE9wTZTAJNlsiJ6CXVC8apuYz6dFGIc1aVTnHi5W3mdfNBjvE7ZAMaz9J6CkDXsrjZAqn-5yiTvOMfa7hWBAzLaL9DLq96R-OfWXlCoeXb581P16Xlk1SQTkboYrxiV5NN9-Rm6X0gTwGR6a-Hle8XLEhHWkemWuP14oQh3hUYcKd-Jy2i83tVqPsJHT3uc9kPdhknHTLJ6W6sivC7thhbiy-xNhsiGRO3g2L3Eujw/http%3A%2F%2Fwww.uniklinikum-dresden.de
Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113


Von: Bernardoni, Fabio
Gesendet: Freitag, 14. Mai 2021 17:28:18
An: freesurfer@nmr.mgh.harvard.edu
Betreff: AW: [Freesurfer] how to visualize statistical maps in FS7.1?

Dear Greve,

thanks for your reply.
These are my steps (I corrected the second):

1) I open the inflated surface:

tksurferfv fsaverage lh inflated

(this successfully displays the inflated left hemisphere of the average subject)

2) I now load the overlay from the freeview window (sig.mgh from a mri_glmfit)

(this successfully overlays the -log(p) statistical map)

3) I would like to threshold the map using FDR<.05. This was possible in 
tksurfer:
https://secure-web.cisco.com/14RYweM71AH5pQm4yA5snEHYyrEVoKp3gpJ8mUW3BNypi7NSOhmp_YRd_jgi1SujzPXH9cIwy0Jernwep4nXrHFntFwpmUGWaIX6TS3NaUOhiQOpi-4w3nsq0bzphVsDjhFHhzNZiBY2LmWmseyLnHL2_5Ush2yKkKt5RdI2Rb74ulrrCLToWDqAnLUM0q_qlRi1RA239cuSMcBgPwpPvJtGGN411DfZewDIyQVbpNY2MLzO1iONzbuI6zyeP0zy7lFjVCoM-4HlMIAnGtBBf0Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FTkSurferGuide%2FTkSurferWorkingWithData%2FTkSurferOverlay

however no such option appears in tksurferfv / freeview

Any hint at this point?

Thanks a lot

Fabio


Dr. Fabio Bernardoni
wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences
http://secure-web.cisco.com/15vnpAEjrPYiKn6yEt0jIUfHx8_4Erx_TvQU05r-dRGFvX5o0_mKiLNQoOoY_DiUFEu3Zb0adehInmHSUaelrON7US4wQ_sWBoQxe2WEPWflAevksiDhq9xUM0HpqhFyVYQ_E6lAcMbhVCVy7BrdLpkrKVNjZklIfxcHcWr5x_R8nAnO3kseYCYgupaYK0YfQU5rXE3-xyfRoCRuDtLtXKnJmnAG9REL9uq0BV_7ZXuM239yt3PhScBv-jdmCWqnVKhzsluD3IrIBTh6UsOy7mQ/http%3A%2F%2Fwww.transdenlab.de%2F;
 
http://secure-web.cisco.com/1PoiqfrNJCTGfMCCkQlttMgDYdjJ_kf3kZ8cHx_f-PnnR1ou9CYrXL4wwpARdd5jBIoEyyH6WRwiGcI2zF0MEzpoexufmjhvKmf_TJMFBg6Cielu-V9qKgk7jDZWTcDm2ciqEtHGLSlLLw-eqLWYalhfAFef1y44MmoHa3utLtAl3loyhlAUlPlAjROXw1deJfxT8nmYTPE19cdW9XGZWokm5kWZ2Nqc_Stox4LWVgzrO1P3Dxj11oUM0MCPkWo0tV7otPW3zFFqjc20pMEyZRA/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm
+49 (0351) 458-5245
Universitätsklinikum Carl Gustav Carus
an der Technischen Universität Dresden
Anstalt des öffentlichen Rechts des Freistaates Sachsen
Fetscherstraße 74, 01307 Dresden
http://secure-web.cisco.com/1riQaRreNdNrwHCBcJyC31n1f-pTKoB2pPlPL__pKwfPnlE9wTZTAJNlsiJ6CXVC8apuYz6dFGIc1aVTnHi5W3mdfNBjvE7ZAMaz9J6CkDXsrjZAqn-5yiTvOMfa7hWBAzLaL9DLq96R-OfWXlCoeXb581P16Xlk1SQTkboYrxiV5NN9-Rm6X0gTwGR6a-Hle8XLEhHWkemWuP14oQh3hUYcKd-Jy2i83tVqPsJHT3uc9kPdhknHTLJ6W6sivC7thhbiy-xNhsiGRO3g2L3Eujw/http%3A%2F%2Fwww.uniklinikum-dresden.de

Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk
Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner
USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

http://secure-web.cisco.com/1riQaRreNdNrwHCBcJyC31n1f-pTKoB2pPlPL__pKwfPnlE9wTZTAJNlsiJ6CXVC8apuYz6dFGIc1aVTnHi5W3mdfNBjvE7ZAMaz9J6

Re: [Freesurfer] Cerebellum Segementation

2021-05-14 Thread Zollei, Lilla,Ph.D. 
Hi Akila,
Have you run recon_all on your structural data?
Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Friday, May 14, 2021 10:35 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Cerebellum Segementation


External Email - Use Caution

External Email - Use Caution

Hello Experts!



This is the first time I am doing tractography and my aim is to do it 
specifically for the cerebellum. I saw online that FreeSurfurer can segment the 
cerebellum, to create the ROI but I’m not entirely sure how to go about this. 
So far I have done the pre-processing, co-registration onto diffusion space and 
created FOD. It would be great if you could give me advice and any feedback 
about the pipeline.



Thanks for your help!



Regards,

Akila
___
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 http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
please contact the sender and properly dispose of the e-mail.
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] Cerebellum Segementation

2021-05-14 Thread A.R. Sekar 
External Email - Use Caution

Hey,

Thanks for your message. Yes I have!

Akila

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Zollei, Lilla,Ph.D. 

Date: Friday, 14 May 2021 at 16:44
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Cerebellum Segementation
Hi Akila,
Have you run recon_all on your structural data?
Lilla

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of A.R. Sekar 

Sent: Friday, May 14, 2021 10:35 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Cerebellum Segementation


External Email - Use Caution

External Email - Use Caution

Hello Experts!



This is the first time I am doing tractography and my aim is to do it 
specifically for the cerebellum. I saw online that FreeSurfurer can segment the 
cerebellum, to create the ROI but I’m not entirely sure how to go about this. 
So far I have done the pre-processing, co-registration onto diffusion space and 
created FOD. It would be great if you could give me advice and any feedback 
about the pipeline.



Thanks for your help!



Regards,

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

Re: [Freesurfer] FreeSurfer error when running Hippocampal Subfields

2021-05-14 Thread Iglesias Gonzalez, Juan E. 
Dear Joana,
Is it possibly that Python changes somehow that libraries that are loaded, 
compared with the command line?
Cheers,
/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com

On May 14, 2021, at 06:06, Joana Collet i Fàbregas 
mailto:joana.col...@gmail.com>> wrote:


External Email - Use Caution

Good morning,

I am a Biomedical Engineering Student at Universitat de Barcelona and I am 
creating a python script that has a Watchdog which detects new patients in a 
specific folder, and we want it to run FS and Hippocampal Subfields. The FS 
runs properly, but when the script arrives to the Hippocampal Subfields 
command, it breaks.

When using the FreeSurfer's Hippocampal Subfields from a python script after 
running FS recon-all right before, the processing is not performed due to the 
error shown in the attatched file. However, when running the Hippocampal 
Subfields from the terminal it does work.

We have even tried to create a watchdog only for the Hippocampal Subfields, and 
when we move a folder obtained after running FS to a specific folder, it also 
runs properly. It is only when it is concatenated with FS that it does not work.

We have contacted MathWorks Support, but they told us to reach you. The Matlab 
versions we have are Matlab_R2020a and Matlab_R2014b.

Thanks a lot,

Joana Collet
___
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
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 http://www.massgeneralbrigham.org/complianceline . If 
the e-mail was sent to you in error but does not contain patient information, 
please contact the sender and properly dispose of the e-mail.
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 error when running Hippocampal Subfields

2021-05-14 Thread Joana Collet i Fàbregas 
External Email - Use Caution

Dear Juan Eugenio,

I'm not sure what you mean. In Python I use os.system() to run the
recon-all command from the command line.
Thanks!

Joana

El dv., 14 de maig 2021, 21:04, Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu> va escriure:

> Dear Joana,
> Is it possibly that Python changes somehow that libraries that are loaded,
> compared with the command line?
> Cheers,
> /E
>
> Juan Eugenio Iglesias
> Senior research fellow
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
> http://secure-web.cisco.com/148BToGpABivasWCgZR8rJMojzoD19lp4xSo0ku22rTNs46gi8eSQpxJJP6k6M4j5RKqRIKorP1-NtqedAacoQmEWnd8tz7Vpdfvp4n5xyzeV6jiUsTOjsuVZzv-qlc7NyV8dUlH8F8-il7vz5LfdbM8Fc5cE8WMR7k-VMx3r06GDDpq7BuAYFAW3uP54OD40bss37bbnQbVpyCeoZ7nJBWZdd6OefdWUCyQhy6OO9JK6dBHQjwvzXZyflpzJfxOHuNuGSCJc9x6KB1mnmc5tdw/http%3A%2F%2Fwww.jeiglesias.com
>
> On May 14, 2021, at 06:06, Joana Collet i Fàbregas 
> wrote:
>
> External Email - Use Caution
>
> Good morning,
>
> I am a Biomedical Engineering Student at Universitat de Barcelona and I am
> creating a python script that has a Watchdog which detects new patients in
> a specific folder, and we want it to run FS and Hippocampal Subfields. The
> FS runs properly, but when the script arrives to the Hippocampal Subfields
> command, it breaks.
>
> When using the FreeSurfer's Hippocampal Subfields from a python script
> after running FS recon-all right before, the processing is not performed
> due to the error shown in the attatched file. However, when running the
> Hippocampal Subfields from the terminal it does work.
>
> We have even tried to create a watchdog only for the Hippocampal
> Subfields, and when we move a folder obtained after running FS to a
> specific folder, it also runs properly. It is only when it is concatenated
> with FS that it does not work.
>
> We have contacted MathWorks Support, but they told us to reach you. The
> Matlab versions we have are Matlab_R2020a and Matlab_R2014b.
>
> Thanks a lot,
>
> Joana Collet
>  Text Editor (1).pdf>___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1ZNwealvi1p5F7stWF1RPAb9qsbw9U-FAN7fNadO_R0oPjoIYIEsfGd9sjTXC7QnBjtJMqXEp_AWV8QFL7ENlQ079ucxrSY89_f3RjcPHEy3Sv4wdKHCZrsFYudFvdgXNU1NP6vLxzDiMG2WejeiItyW49K8p3Z29LqCUe32Tit3EZmbK9eSbppg_WRvSKjLPMwZmVp3oMskEfnsGUSMgR8LfhT0kzKntXVSlBRfh_Ccy9QolbN08-rEvOYcAYfy8TGMwe0JdYdqKUK9aPL7vBA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1ZNwealvi1p5F7stWF1RPAb9qsbw9U-FAN7fNadO_R0oPjoIYIEsfGd9sjTXC7QnBjtJMqXEp_AWV8QFL7ENlQ079ucxrSY89_f3RjcPHEy3Sv4wdKHCZrsFYudFvdgXNU1NP6vLxzDiMG2WejeiItyW49K8p3Z29LqCUe32Tit3EZmbK9eSbppg_WRvSKjLPMwZmVp3oMskEfnsGUSMgR8LfhT0kzKntXVSlBRfh_Ccy9QolbN08-rEvOYcAYfy8TGMwe0JdYdqKUK9aPL7vBA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 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
> http://secure-web.cisco.com/1LPIYFofpHCLeAMGUT9l-1tpoLMMxCLWOMnsuMuz9kqlmTZIouSwMWx79BnOdQrIE8QPPcsKrtKeOpcNtK9XVB5qt-HYHdqUzGL6L57WuaSbJ5f-GXz_sbtJm_XNlPic3dewisD6zig0XJnOscCnNRMqYpuCIIuUkf1faftLEo5mQpSM6i1zXs1KaU5YWG9GsqC416sAHMkaEOr2E5JLlirPamtVzSk9vvJIEiFWiYJ-IkC7t6bh1sP1hv9x6y6JKz9NbIFMVM0ZgLx3kJwTJOw/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
>  . If the e-mail was sent
> to you in error but does not contain patient information, please contact
> the sender and properly dispose of the e-mail.
> 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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] FreeSurfer Error: xx: Subscript out of range

2021-05-14 Thread Shanika Jayakody 
External Email - Use Caution

Dear FreeSurfer team

I have been trying to run trac pre-processing on some subjects but keep getting 
the error "xx: Subscript out of range."
The number of data entries in bvecs/bval files are similar to the .nii file and 
I have used configuration files similar to the ones I have been using
Attached here are my configuration file and trac-log file.
Any suggestion/advice is really appriciated

Thank you
Regards
Oshadi
Fri May 14 15:52:27 EDT 2021
/home/helena/Documents/freesurfer/subjects
/home/helena/Documents/freesurfer/bin/trac-all
-prep -c Config_50.txt
Subject 50
SUBJECTS_DIR /home/helena/Documents/freesurfer/subjects
FREESURFER_HOME /home/helena/Documents/freesurfer
Actual FREESURFER_HOME /home/helena/Documents/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
helena
VENEU313BU
Linux VENEU313BU 4.15.0-142-generic #146~16.04.1-Ubuntu SMP Tue Apr 13 09:27:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  256777 
maxlocks unlimited
maxsignal256777 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   6580684810088932 8698336  1246164701958054777948
Swap:999420   0  999420


Program versions:
$Id: trac-all,v 1.60.2.1 2016/12/20 17:04:05 zkaufman Exp $
mri_convert.bin --all-info 
ProgramName: mri_convert.bin  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/05/14-19:52:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $  User: helena  Machine: VENEU313BU  Platform: Linux  PlatformVersion: 4.15.0-142-generic  CompilerName: GCC  CompilerVersion: 40400 
FLIRT version 6.0
$Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $
$Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $
ProgramName: dmri_motion  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/05/14-19:52:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: helena  Machine: VENEU313BU  Platform: Linux  PlatformVersion: 4.15.0-142-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_train  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/05/14-19:52:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: helena  Machine: VENEU313BU  Platform: Linux  PlatformVersion: 4.15.0-142-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_paths  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/05/14-19:52:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: helena  Machine: VENEU313BU  Platform: Linux  PlatformVersion: 4.15.0-142-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_pathstats  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/05/14-19:52:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: helena  Machine: VENEU313BU  Platform: Linux  PlatformVersion: 4.15.0-142-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_mergepaths  ProgramArguments: --all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2021/05/14-19:52:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: helena  Machine: VENEU313BU  Platform: Linux  PlatformVersion: 4.15.0-142-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: dmri_group  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2021/05/14-19:52:27-GMT  BuildTimeStamp: Jan 18 2017 16:38:58  CVS:   User: helena  Machine: VENEU313BU  Platform: Linux  PlatformVersion: 4.15.0-142-generic  CompilerName: GCC  CompilerVersion: 40400 


New invocation of trac-preproc


helena
VENEU313BU
Linux VENEU313BU 4.15.0-142-generic #146~16.04.1-Ubuntu SMP Tue Apr 13 09:27:15 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  256777 
maxlocks unlimited
maxsignal256777 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

  totalusedfree  shared  buff/cache   available
Mem:   6580684810089504 8697764  1246164701958054777376
Swap:999420   0  999420

#-
/home/helena/Documents/freesurfer/bin/trac-preproc 
#-
#@# Image corrections Fri May 14 15:52:27 EDT 2021
mri_convert --bvec-voxel /home/helena/Documents/freesurfer/subjects/50/DICOM_WIP_111_DT

Re: [Freesurfer] FreeSurfer error when running Hippocampal Subfields

2021-05-14 Thread Iglesias Gonzalez, Juan E. 
Yes, but that doesn’t guarantee that the (library) environment is the same as 
when you run something from the terminal.
I’m CCing Andrew Hoppes to see if he can assist.
Cheers,
/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com

On May 14, 2021, at 15:22, Joana Collet i Fàbregas 
mailto:joana.col...@gmail.com>> wrote:


External Email - Use Caution

Dear Juan Eugenio,

I'm not sure what you mean. In Python I use os.system() to run the recon-all 
command from the command line.
Thanks!

Joana

El dv., 14 de maig 2021, 21:04, Iglesias Gonzalez, Juan E. 
mailto:jiglesiasgonza...@mgh.harvard.edu>> 
va escriure:
Dear Joana,
Is it possibly that Python changes somehow that libraries that are loaded, 
compared with the command line?
Cheers,
/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
http://www.jeiglesias.com

On May 14, 2021, at 06:06, Joana Collet i Fàbregas 
mailto:joana.col...@gmail.com>> wrote:


External Email - Use Caution

Good morning,

I am a Biomedical Engineering Student at Universitat de Barcelona and I am 
creating a python script that has a Watchdog which detects new patients in a 
specific folder, and we want it to run FS and Hippocampal Subfields. The FS 
runs properly, but when the script arrives to the Hippocampal Subfields 
command, it breaks.

When using the FreeSurfer's Hippocampal Subfields from a python script after 
running FS recon-all right before, the processing is not performed due to the 
error shown in the attatched file. However, when running the Hippocampal 
Subfields from the terminal it does work.

We have even tried to create a watchdog only for the Hippocampal Subfields, and 
when we move a folder obtained after running FS to a specific folder, it also 
runs properly. It is only when it is concatenated with FS that it does not work.

We have contacted MathWorks Support, but they told us to reach you. The Matlab 
versions we have are Matlab_R2020a and Matlab_R2014b.

Thanks a lot,

Joana Collet
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
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 MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://www.massgeneralbrigham.org/complianceline
 . If the e-mail was sent to you in error but does not contain patient 
information, please contact the sender and properly dispose of the e-mail.
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 t