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. 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-qSgoFL3F5efz5cMI8VXYVwf6R9qKpKCswVpb5vy1yHm5Pps1SX5R3RLuSscgeuoaKi7Om2j5M4NUidupsaNsbWGfIHXVY0Xrq6sSHFakOOr30sdfDpB3B4tyPu99sJP46YUIvfv7bWBNCzVjVdKL4vTnKdcvCmE1nEYKqhFdj1zHOepNi67IfZpTND0-2C8hEQ18iU9WkHpiDlQfBmRB4zN7VqrRF6Xunz9-KIYAP9hfiFHPXiQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1JdzV_eLGjN4P1uKYNQWCZu9cvVf9owfxF4-qSgoFL3F5efz5cMI8VXYVwf6R9qKpKCswVpb5vy1yHm5Pps1SX5R3RLuSscgeuoaKi7Om2j5M4NUidupsaNsbWGfIHXVY0Xrq6sSHFakOOr30sdfDpB3B4tyPu99sJP46YUIvfv7bWBNCzVjVdKL4vTnKdcvCmE1nEYKqhFdj1zHOepNi67IfZpTND0-2C8hEQ18iU9WkHpiDlQfBmRB4zN7VqrRF6Xunz9-KIYAP9hfiFHPXiQ/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/1KDmkKd_z_ugUNK92Dhb-G0c-aOALsTRbaL-6Ht4EABO7NtBqZMVV1RwlQb3eJCDtZWRknfP_q-TTrtxVozcGxc3pMbGO_tw7cX6hC_xbZwm-GCBIqDPigWrpYHfDy_HVyv-iQn782SAhW9VzNSqMxWS7vW8b_RFTdbBnTua77TYtF3vWuDlfvwMb0zp9cgzTkxVvJcn4Ji3v4Hkj_RRb28Pu8PCFkGeztSqgQZ_VP8vA7rCNj-tfChrzqLykHqbKzWlZPLFg7_aNOvD4nogo-Q/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://secure-web.cisco.com/1LD9SSlOyQuhvXvxH71fQf9znxmNpw0EgmusvdXjKqnkQINMc8PdcJm0k2kx3XXdO6dTL1LFxub0ZLjVTFEmCZum3bmQrZPmjosHAWnqiimI8oEUNvVkxBlqR9VIzYvZPsSWCJSB-GKEA0mOAcFFwr-eNe3kDgzUg_TbX9xSmK74zEPPeaZbThxolXmmetVU3xjTisHSEYnXI99M9atCTS7Jh-29KzHyKNbAB-nlQu-sCDuB6Irx5vvnYEXH_ugkASOx9HdWy0bZyBfmvxOjrkQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
