how to visualize statistical maps in FS7.1?

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Bernardoni, Fabio

12 May 2021 12 May '21

6:06 a.m.

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 It seems, however, it is no longer maintained.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-X9TSsF6...

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-kcGEyM5xIf9EYKEBdxq9jOYgp4LWrcrsRqW2VW0t2XhE...; http://secure-web.cisco.com/1xug_1JvXuCXLAVwiFYmOgWpcXQT14Ee7lkNin2N9gXlkJe_... +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/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EB...

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/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EB... 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

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Douglas N. Greve

13 May 13 May

11:11 a.m.

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 It seems, however, it is no longer maintained.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-X9TSsF6...

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-kcGEyM5xIf9EYKEBdxq9jOYgp4LWrcrsRqW2VW0t2XhE...; http://secure-web.cisco.com/1xug_1JvXuCXLAVwiFYmOgWpcXQT14Ee7lkNin2N9gXlkJe_... +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/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EB...

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/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EB... 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

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

Bernardoni, Fabio

14 May 14 May

11:28 a.m.

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/1Zl2C3ogXmhGUNaxqBtskesqKl5yJdBXWaIvAlRRQc78fBL...

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/1YX3ipy7sscoJinbT24JROYpvfMLxUzj6WI8zTOix4cybxxC...; http://secure-web.cisco.com/1FLummlkSSdFqIQV8zg9pbFpjFgeXVHEbYHk2pa_UduhDt_b... +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-e0tKnEcSkhso...

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-e0tKnEcSkhso... 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Douglas N. Greve dgreve@MGH.HARVARD.EDU 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-X9TSsF6...

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-kcGEyM5xIf9EYKEBdxq9jOYgp4LWrcrsRqW2VW0t2XhE...; http://secure-web.cisco.com/1xug_1JvXuCXLAVwiFYmOgWpcXQT14Ee7lkNin2N9gXlkJe_... +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/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EB...

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/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EB... 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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1-SvMTKzZtLe7bAK0kvSIlup0SUwQQYrfH1hzW-yIqmG7P8...

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1-SvMTKzZtLe7bAK0kvSIlup0SUwQQYrfH1hzW-yIqmG7P8... 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/1m_2QYj8VHVFyyBlCSpXVgHKO29ucAOZyy4dusgaNPCErc3U... . 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.

Bernardoni, Fabio

11:35 a.m.

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-dRGFvX5o...; http://secure-web.cisco.com/1PoiqfrNJCTGfMCCkQlttMgDYdjJ_kf3kZ8cHx_f-PnnR1ou... +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__pKwfPnlE9...

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__pKwfPnlE9... 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/14RYweM71AH5pQm4yA5snEHYyrEVoKp3gpJ8mUW3BNypi7N...

however no such option appears in tksurferfv / freeview

Any hint at this point?

Thanks a lot

Fabio

Dr. Fabio Bernardoni wiss. Mitarbeiter

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

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-X9TSsF6...

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-kcGEyM5xIf9EYKEBdxq9jOYgp4LWrcrsRqW2VW0t2XhE...; http://secure-web.cisco.com/1xug_1JvXuCXLAVwiFYmOgWpcXQT14Ee7lkNin2N9gXlkJe_... +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/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EB...

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/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EB... 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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1JdzV_eLGjN4P1uKYNQWCZu9cvVf9owfxF4-qSgoFL3F5ef...

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1JdzV_eLGjN4P1uKYNQWCZu9cvVf9owfxF4-qSgoFL3F5ef... 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/1KDmkKd_z_ugUNK92Dhb-G0c-aOALsTRbaL-6Ht4EABO7NtB... . 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.

Bernardoni, Fabio

11 Jun 11 Jun

11:53 a.m.

External Email - Use Caution

dear all

even though on the official webpage it is advised to use freeview to display statistical maps because tksurfer is considered obsolete/not maintained in freesurfer 7, I am unable to reproduce the same figures, even when using tksurferfv.

one feature that is missing but can be reproduced using mri_fdr is FDR thresholding. however, it is not clear to me how to produce a decent color scale given a threshold computed by mri_fdr or any other means, which indicates the threshold.

could someone please suggest how to edit the color scale in freeview? or whether there is an alternative software to display the overlays/statistical maps produced by freesurfer?

thank you very much in advance!

fabio

Dr. Fabio Bernardoni wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1NUA3Kn39JuhF9hBZYddG5zC7EUE779Ca85qGI3CWyMQGgtc...; http://secure-web.cisco.com/14qCxqn3snsuFXdZvB5lycE4FPyFND_EXl-CJ4_Vot9lSJiT... +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/1JVU6ptyi0UylqscvJdbls1kdBS1xucJG_cmj67TO-3RTuRu...

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/1JVU6ptyi0UylqscvJdbls1kdBS1xucJG_cmj67TO-3RTuRu... 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Bernardoni, Fabio Fabio.Bernardoni@uniklinikum-dresden.de Gesendet: Freitag, 14. Mai 2021 17:35:25 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] how to visualize statistical maps in FS7.1?

External Email - Use Caution

Ok I found a solution using separately mri_fdr

thanks anyway!

Dr. Fabio Bernardoni wiss. Mitarbeiter

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

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/14RYweM71AH5pQm4yA5snEHYyrEVoKp3gpJ8mUW3BNypi7N...

however no such option appears in tksurferfv / freeview

Any hint at this point?

Thanks a lot

Fabio

Dr. Fabio Bernardoni wiss. Mitarbeiter

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

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-X9TSsF6...

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-kcGEyM5xIf9EYKEBdxq9jOYgp4LWrcrsRqW2VW0t2XhE...; http://secure-web.cisco.com/1xug_1JvXuCXLAVwiFYmOgWpcXQT14Ee7lkNin2N9gXlkJe_... +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/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EB...

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/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EB... 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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1JdzV_eLGjN4P1uKYNQWCZu9cvVf9owfxF4-qSgoFL3F5ef...

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1LD9SSlOyQuhvXvxH71fQf9znxmNpw0EgmusvdXjKqnkQIN...

Wang, Ruopeng

20 Jun 20 Jun

11:39 a.m.

After you load the overlay onto the surface, you can click on “Configure Overlay” button on the left pane to adjust color scale and thresholds for the overlay.

Ruopeng

...

On Jun 11, 2021, at 11:53 AM, Bernardoni, Fabio Fabio.Bernardoni@uniklinikum-dresden.de wrote:
   External Email - Use Caution        
dear all

even though on the official webpage it is advised to use freeview to display statistical maps because tksurfer is considered obsolete/not maintained in freesurfer 7, I am unable to reproduce the same figures, even when using tksurferfv.

one feature that is missing but can be reproduced using mri_fdr is FDR thresholding. however, it is not clear to me how to produce a decent color scale given a threshold computed by mri_fdr or any other means, which indicates the threshold.

could someone please suggest how to edit the color scale in freeview? or whether there is an alternative software to display the overlays/statistical maps produced by freesurfer?

thank you very much in advance!

fabio

Dr. Fabio Bernardoni wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1NUA3Kn39JuhF9hBZYddG5zC7EUE779Ca85qGI3CWyMQGgtc...; http://secure-web.cisco.com/14qCxqn3snsuFXdZvB5lycE4FPyFND_EXl-CJ4_Vot9lSJiT... +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/1JVU6ptyi0UylqscvJdbls1kdBS1xucJG_cmj67TO-3RTuRu...

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/1JVU6ptyi0UylqscvJdbls1kdBS1xucJG_cmj67TO-3RTuRu... 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Bernardoni, Fabio Fabio.Bernardoni@uniklinikum-dresden.de Gesendet: Freitag, 14. Mai 2021 17:35:25 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] how to visualize statistical maps in FS7.1?
   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-dRGFvX5o...; http://secure-web.cisco.com/1PoiqfrNJCTGfMCCkQlttMgDYdjJ_kf3kZ8cHx_f-PnnR1ou... +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__pKwfPnlE9...

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__pKwfPnlE9... 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):

I open the inflated surface:

tksurferfv fsaverage lh inflated

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

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

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

I would like to threshold the map using FDR<.05. This was possible in tksurfer:

https://secure-web.cisco.com/14RYweM71AH5pQm4yA5snEHYyrEVoKp3gpJ8mUW3BNypi7N...

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-dRGFvX5o...; http://secure-web.cisco.com/1PoiqfrNJCTGfMCCkQlttMgDYdjJ_kf3kZ8cHx_f-PnnR1ou... +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__pKwfPnlE9...

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__pKwfPnlE9... 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Douglas N. Greve dgreve@MGH.HARVARD.EDU 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-X9TSsF6...

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-kcGEyM5xIf9EYKEBdxq9jOYgp4LWrcrsRqW2VW0t2XhE...; http://secure-web.cisco.com/1xug_1JvXuCXLAVwiFYmOgWpcXQT14Ee7lkNin2N9gXlkJe_... +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/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EB...

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/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EB... 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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1JdzV_eLGjN4P1uKYNQWCZu9cvVf9owfxF4-qSgoFL3F5ef...
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1JdzV_eLGjN4P1uKYNQWCZu9cvVf9owfxF4-qSgoFL3F5ef... 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/1KDmkKd_z_ugUNK92Dhb-G0c-aOALsTRbaL-6Ht4EABO7NtB... . 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://secure-web.cisco.com/1LD9SSlOyQuhvXvxH71fQf9znxmNpw0EgmusvdXjKqnkQIN...

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

Bernardoni, Fabio

15 Jul 15 Jul

11:38 a.m.

External Email - Use Caution

Dear Ruopeng,

thanks for looking into this, and sorry for ma delayed reply. I have just read your answer.

I can certainly do what you suggest, but the color bar is a bit confusing, see attachment. Somehow it suggests that the threshold is 0.767, when indeed it is 1.23 (these numbers are chosen exclusively to describe the software problem and the maps represented have no sense).

When using the color bar in tksurfer the numbers shown intuitively revealed the threshold used in the map. What would you advice to do?

Thanks

Fabio

Dr. Fabio Bernardoni wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1XKwsmi3avefS71WvESrS21dlvouLIT0a0hkwdvOxefdlFmx...; http://secure-web.cisco.com/1tm9-tiaDYHfSJxmupDoJsEMPBRy1RjRDXH70KOJHesSeR9f... +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/1aPrA0y3GrdBT34N-2egT1gVzu2Du4EWWX9OxluSEzA0Z6lm...

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/1aPrA0y3GrdBT34N-2egT1gVzu2Du4EWWX9OxluSEzA0Z6lm... 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Wang, Ruopeng RWANG4@MGH.HARVARD.EDU Gesendet: Sonntag, 20. Juni 2021 17:39:57 An: Freesurfer support list Betreff: Re: [Freesurfer] how to visualize statistical maps in FS7.1?

After you load the overlay onto the surface, you can click on “Configure Overlay” button on the left pane to adjust color scale and thresholds for the overlay.

Ruopeng

...

On Jun 11, 2021, at 11:53 AM, Bernardoni, Fabio Fabio.Bernardoni@uniklinikum-dresden.de wrote:
   External Email - Use Caution
dear all

even though on the official webpage it is advised to use freeview to display statistical maps because tksurfer is considered obsolete/not maintained in freesurfer 7, I am unable to reproduce the same figures, even when using tksurferfv.

one feature that is missing but can be reproduced using mri_fdr is FDR thresholding. however, it is not clear to me how to produce a decent color scale given a threshold computed by mri_fdr or any other means, which indicates the threshold.

could someone please suggest how to edit the color scale in freeview? or whether there is an alternative software to display the overlays/statistical maps produced by freesurfer?

thank you very much in advance!

fabio

Dr. Fabio Bernardoni wiss. Mitarbeiter

Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1NUA3Kn39JuhF9hBZYddG5zC7EUE779Ca85qGI3CWyMQGgtc...; http://secure-web.cisco.com/14qCxqn3snsuFXdZvB5lycE4FPyFND_EXl-CJ4_Vot9lSJiT... +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/1JVU6ptyi0UylqscvJdbls1kdBS1xucJG_cmj67TO-3RTuRu...

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/1JVU6ptyi0UylqscvJdbls1kdBS1xucJG_cmj67TO-3RTuRu... 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Bernardoni, Fabio Fabio.Bernardoni@uniklinikum-dresden.de Gesendet: Freitag, 14. Mai 2021 17:35:25 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] how to visualize statistical maps in FS7.1?
   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-dRGFvX5o...; http://secure-web.cisco.com/1PoiqfrNJCTGfMCCkQlttMgDYdjJ_kf3kZ8cHx_f-PnnR1ou... +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__pKwfPnlE9...

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__pKwfPnlE9... 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):

I open the inflated surface:

tksurferfv fsaverage lh inflated

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

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

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

I would like to threshold the map using FDR<.05. This was possible in tksurfer:

https://secure-web.cisco.com/14RYweM71AH5pQm4yA5snEHYyrEVoKp3gpJ8mUW3BNypi7N...

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-dRGFvX5o...; http://secure-web.cisco.com/1PoiqfrNJCTGfMCCkQlttMgDYdjJ_kf3kZ8cHx_f-PnnR1ou... +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__pKwfPnlE9...

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__pKwfPnlE9... 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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Douglas N. Greve dgreve@MGH.HARVARD.EDU 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-X9TSsF6...

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-kcGEyM5xIf9EYKEBdxq9jOYgp4LWrcrsRqW2VW0t2XhE...; http://secure-web.cisco.com/1xug_1JvXuCXLAVwiFYmOgWpcXQT14Ee7lkNin2N9gXlkJe_... +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/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EB...

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/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EB... 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

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1JdzV_eLGjN4P1uKYNQWCZu9cvVf9owfxF4-qSgoFL3F5ef...
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_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1d7S_FPVF9g9QOT2uttuJJmPp954q9bxn666piOk5dr5yBf... 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/16bRlLFXKMf0wMNHpypQPIu4lgPXUnbP5uCGB3KgvWmnwnz9... . 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.

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Bernardoni, Fabio
Douglas N. Greve
Wang, Ruopeng