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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 CautionDear 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 It seems, however, it is no longer maintained.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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