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.bernard...@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/1NUA3Kn39JuhF9hBZYddG5zC7EUE779Ca85qGI3CWyMQGgtceMJDZRWhouZ5WGjYJWj9bwKrD2fD8s-hYFwlM9Zb7PnHApqOOdsXMN_UqKlRrAimZGaAbHyNmcB9eQc5bFAwPScLDl6teibcOsvSTEnICFgvqooR9lO2wtAQTJ5FeXCgJ_SpT53obkUl22C99Qs40AAaX_Wl-lb7XLeXtAn2E4QG0UtoS7p7UeyqVg_TLcctdVMNC-o4N0Uy1K879qlpx8J4ph1VuwogyQIlbGA/http%3A%2F%2Fwww.transdenlab.de%2F; > > http://secure-web.cisco.com/14qCxqn3snsuFXdZvB5lycE4FPyFND_EXl-CJ4_Vot9lSJiTnBFfpJazexQgemAFSqoGm7CBIyEnExxeRG6zWhYfzffjDt7l2n5yMtZAefgBXdkiV56cfJbXtHdHuWPQFlvInkSQIulWLx6mp6mbDfqfTojWarCOggU4inOp1-_BNPn9sKuPQxbme2JtgDgI3jrhzF1cGekZtMUl4O9mmuQgm5kH9QvITIy1-mBcFsoBz1x2MSpGocBouBWImztww-pm8hUehycRbu2-ob0_I6w/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/1JVU6ptyi0UylqscvJdbls1kdBS1xucJG_cmj67TO-3RTuRuqiG-X_1kQ8TK1iQT17dO0BYDk3mwMI5uwOMVyh7Q6C3RX_zAtLpzSDcnxl2q686FdPz6O_RCH2cMTW938-h5U6VP8oUS1kirsQCWWUQeImIkIv7P9eNcU8CQieJiLKt7tK--KMZoYDdnNILXhciGdXCnfdWPj4tzQ1dsStvviGy3pAqt7Yx6E1dZZ7-N6K0UT_hCph8stL0E4nrEX_jVenDNhXOgEjPbUf9Nq7Q/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/1JVU6ptyi0UylqscvJdbls1kdBS1xucJG_cmj67TO-3RTuRuqiG-X_1kQ8TK1iQT17dO0BYDk3mwMI5uwOMVyh7Q6C3RX_zAtLpzSDcnxl2q686FdPz6O_RCH2cMTW938-h5U6VP8oUS1kirsQCWWUQeImIkIv7P9eNcU8CQieJiLKt7tK--KMZoYDdnNILXhciGdXCnfdWPj4tzQ1dsStvviGy3pAqt7Yx6E1dZZ7-N6K0UT_hCph8stL0E4nrEX_jVenDNhXOgEjPbUf9Nq7Q/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 > <freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Bernardoni, Fabio > <fabio.bernard...@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-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__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: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Douglas N. Greve > <dgr...@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-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_blhCQ8oexcOBMTiefsG3_aAP0L5sU_H9y1xYVTw6Wh6hIqLbAa4i4vAgC5EkA-lRurbVwk8nsJ2OkIW9GfadFxibvScxITahbmnRCznxGJlPF-53t2LTXrv5ovrctRRUr3HCbs6q1-FfiwpZbapsJCpLgnVMXDIXmR9FalmQ1tAveKdaDRqfq1X5OnoG5ccMFg/http%3A%2F%2Fwww.transdenlab.de%2F; >> >> http://secure-web.cisco.com/1xug_1JvXuCXLAVwiFYmOgWpcXQT14Ee7lkNin2N9gXlkJe_rVe8WFPk8CrMRmNwa_OuMhrKZXOFFO-FGw4FoQLrEFxfrO0Bmrs52S58GLUHqIsCPDL1IlMhZljPMxwDvqHheBhbH3FY9WwkZleNf0vOcLN7T--LeyLSKHC_sDn8owSIUefCSKVrRFaCMbFr5M04ZXYBHqA2QiHHZt1TpSnAlfoaQMAYejGip5Lnf_rIw4wUFl8P8g9z1Vi1EDDQW72FYV0DvC7gVAebazbP_AQ/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/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EBtyOQOncARekE9xGU6ufm0K3AsWqpT_QNy_QstYzolatBvaWI4t7eMeALTKskxEvWoxokVkLLB4HMJ0YkwdqKEe8ljROpTHIFtyq1qCflRlJTMWaL3-X3wy0Xoc3l8aqALWtblfOLH8ZWHGuYKuFG4ZDS2lawCB8R4FPsst51f44nwNGvWALB0xsX_5W2NQbQ4wnfuAoIXlyw0pV5MKnAhp5Uh9k6uZlMYG5XgZw/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/1ymiT7HwdvqBcrZ2JgPJohlSR2r6RJdo68pLuJ1xGc6Cx6EBtyOQOncARekE9xGU6ufm0K3AsWqpT_QNy_QstYzolatBvaWI4t7eMeALTKskxEvWoxokVkLLB4HMJ0YkwdqKEe8ljROpTHIFtyq1qCflRlJTMWaL3-X3wy0Xoc3l8aqALWtblfOLH8ZWHGuYKuFG4ZDS2lawCB8R4FPsst51f44nwNGvWALB0xsX_5W2NQbQ4wnfuAoIXlyw0pV5MKnAhp5Uh9k6uZlMYG5XgZw/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. 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