External Email - Use Caution Dear Eugenio,
We checked the RAM setting of the Docker container and found it was default using 2GB RAM! Then we set the Maximum RAM up to 16GB and work all done!! Thank you for your patience helping so much! Wish you have a great day! Best regards, Josephine <freesurfer-requ...@nmr.mgh.harvard.edu> 於 2021年6月12日 週六 上午12:01寫道： > Send Freesurfer mailing list submissions to > freesurfer@nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > > https://secure-web.cisco.com/1_MhR_xuFQQ6f3qyQNiH1uM9hERvO8xgb2j3Rov_l0il6hbHNPp-S_Nq-ShOMYmMPxrwl6s13BldUkboAxefLQCI4lReHyl7oRT4tHsad_DN7Q1z2jVWH5t6B2VA0HZAw1kjyiyG7-fPVzHUjRCuZEumVVhvKawGupDt5uRElcg5CKldh2xQgpy6GaYqDv9aehkA5-nMlzyTAurB5pMnvmh2BWic0BiPkiU-uQ_-aETge44C700l0FZHpt5s-xoDP3D11YpxaoEEguvkBOcWxAw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-requ...@nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-ow...@nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: T1 hippocampal subfields exited with ERRORS > (Iglesias Gonzalez, Juan E.) > 2. Open Position: Postdoc or PhD Student for Deep Learning based > Lesion Recognition in human MRI (Dr. rer. nat. Johannes Jungilligens) > 3. Finding equivalent vertices on fsaverage_sym lh and rh > surfaces (Tim Sch?fer) > 4. Re: memory allocation error (Bernardoni, Fabio) > 5. Issues with recon-all hanging (Michael Datko) > 6. Re: how to visualize statistical maps in FS7.1? > (Bernardoni, Fabio) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 11 Jun 2021 11:52:08 +0000 > From: "Iglesias Gonzalez, Juan E." <jiglesiasgonza...@mgh.harvard.edu> > Subject: Re: [Freesurfer] T1 hippocampal subfields exited with ERRORS > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <2e162b79-9558-4942-8b6e-55a7b384d...@mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Dear Josephine, > This is unusual. Could it be possible that you are running out of RAM > memory? Do you have 16GB or more available? > Cheers, > /Eugenio > > On 11 Jun 2021, at 01:39, ??? <ytlin...@g.ntu.edu.tw<mailto: > ytlin...@g.ntu.edu.tw>> wrote: > > > External Email - Use Caution > > Dear Developer and Eugenio, > > We encounter the error at the end of the analysis,it looks like this: > > Smoothing mesh collection with kernel size 0.750000 > .../usr/local/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: > line 40: 499 Killed > /usr/local/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML S013 /data > 0.333333333333333333333333333333333333 > /usr/local/freesurfer/average/HippoSF/atlas/AtlasMesh.gz > /usr/local/freesurfer/average/HippoSF/atlas/AtlasDump.mgz > /usr/local/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt 0.05 > right L-BFGS v21 '/usr/local/freesurfer/bin/fs_run_from_mcr > /usr/local/freesurfer/bin/' 0 > Linux f8e6a6f8a44a 5.10.25-linuxkit #1 SMP Tue Mar 23 09:27:39 UTC 2021 > x86_64 x86_64 x86_64 GNU/Linux > > T1 hippocampal subfields exited with ERRORS at Thu Jun 10 10:22:54 UTC 2021 > > I've attached the log file here, could you help us with this error? Thank > you so much! > > Best regards, > Josephine > > <hippocampal-subfields-T1.log>_______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/1_MhR_xuFQQ6f3qyQNiH1uM9hERvO8xgb2j3Rov_l0il6hbHNPp-S_Nq-ShOMYmMPxrwl6s13BldUkboAxefLQCI4lReHyl7oRT4tHsad_DN7Q1z2jVWH5t6B2VA0HZAw1kjyiyG7-fPVzHUjRCuZEumVVhvKawGupDt5uRElcg5CKldh2xQgpy6GaYqDv9aehkA5-nMlzyTAurB5pMnvmh2BWic0BiPkiU-uQ_-aETge44C700l0FZHpt5s-xoDP3D11YpxaoEEguvkBOcWxAw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/11UezoUxbRTSw8IN8cHHYqv8aztD0H-uJlLFu_b6l5C5QeBH6TxcLE43a-JSEkVWh2O01Yu8Oe2Npp8O0S1_pQaEVEao7UpIoillhAG9NTbe_mPjCJj-yVQ-4HMCKU7FyxINYLbOMTE81PwDzHpcEbmKiuNMshW4TEyWHKtkKyZHCk0y2P3ZG4pPNEGuhvR1rwTYK6YRURO4ElyIk6h-NdXsAJ1nr8KBCROxIeMzLBAZu_fm7v8GUJz5dPCMNoAhiJY1V0Ff0oOQyrBu6K9tUvA/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210611%2F42e5644d%2Fattachment-0001.html > > ------------------------------ > > Message: 2 > Date: Fri, 11 Jun 2021 08:37:35 -0400 > From: "Dr. rer. nat. Johannes Jungilligens" > <johannes.jungillig...@rub.de> > Subject: [Freesurfer] Open Position: Postdoc or PhD Student for Deep > Learning based Lesion Recognition in human MRI > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > < > caaomhor4w9sjpkazogzxs2-x+65omge+2m-fdu1ncdh2paj...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > *Postdoc or PhD Student for Deep Learning based Lesion Recognition in human > MRI* > > available from July 1st, 2021, or later. The position will be embedded in a > three-year project within the Human Centered AI Network (HUMAINE) at > Ruhr-University Bochum (RUB), Germany. The highly interdisciplinary project > deals with the identification and characterization of epilepsy-causing > lesions in MRI images of the brain and their discrimination from > non-epileptogenic lesions. The project is conducted at the epilepsy center > of the university medical center Knappschaftskrankenhaus > (Ruhr-Epileptology, J?rg Wellmer) in close collaboration with the > Bioinformatics group at the Center for Protein Diagnostics RUB (Axel > Mosig). > > The applicant should hold a degree in computer science, physics, or > comparable studies and have experience along with profound theoretical and > practical knowledge of deep learning in the context of three-dimensional > medical imaging, in particular using state-of-the-art frameworks such as > tensorflow of pyTorch. > > We offer an inspiring working environment in well-established > interdisciplinary structures, providing state-of-the-art IT infrastructure > in a highly dynamic interdisciplinary setting with project partners > covering the whole range between medicine, machine learning, sociology, and > business. The salary is that of a full-position scientist according to > German payment standards. > > For further information and application, feel free to contact J?rg Wellmer > ( > joerg.well...@kk-bochum.de) and Axel Mosig (axel.mo...@rub.de). > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/105R6joc6puQbD3W5JLJhWC81-cdRapv34k2qRdHv9uMeRy_24cUDXhbXZ6B3buYyiTQznY4OrnXT_PDL0rQGok3kGqZftbHIqmC8SNg7iDiMYPTGS88MbZoed3xxYSkPdJcmdJg72-VNcuhTrXAw9fjQAKA2nOpOp0TSCcyBva9OaRzER3fyvkXm8Z4oJbrxopTHItcX5bPDwC25BEv05RYjQzFZR-v2wM3jklH_tYMulUC_gsu0GOGmKBykvL91P4MrKO-e59yaXpgZvNGiLQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210611%2F7eceee0d%2Fattachment-0001.html > > ------------------------------ > > Message: 3 > Date: Fri, 11 Jun 2021 16:01:44 +0200 (CEST) > From: Tim Sch?fer <ts...@rcmd.org> > Subject: [Freesurfer] Finding equivalent vertices on fsaverage_sym lh > and rh surfaces > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <1290876552.38407.1623420104...@ox.hosteurope.de> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Dear FreeSurfer experts, > > for the 'fsaverage_sym' template that comes with FreeSurfer, I would like > to find a mapping between equivalent vertices (i.e., vertices in the same > anatomical position) between the left and right hemispheres. > > By "equivalent" I mean identical anatomical positions. I noticed, for > example, that vertex 500 in the file fsaverage_sym/surf/lh.white and vertex > 500 in the file fsaverage_sym/surf/rh.white are not at equivalent > anatomical points. > > I feel this mapping must be documented somewhere or there is an obvious > way to get it that I am currently overlooking, so I thought I'd ask here. > > Thanks in advance, > > Tim > > -- > Dr. Tim Sch?fer > Postdoc Computational Neuroimaging > Department of Child and Adolescent Psychiatry, Psychosomatics and > Psychotherapy > University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany > > > > ------------------------------ > > Message: 4 > Date: Fri, 11 Jun 2021 15:10:41 +0000 > From: "Bernardoni, Fabio" <fabio.bernard...@uniklinikum-dresden.de> > Subject: Re: [Freesurfer] memory allocation error > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <4b5ecebd01af4ac8b5317c9c24f5f...@uniklinikum-dresden.de> > Content-Type: text/plain; charset="iso-8859-1" > > External Email - Use Caution > > dear all, > > is there any progress on this issue? can I send more information to help > with debugging? judging from the other entries of the mailing list this is > not an issue that concerns only me. > > thank you for your attention, > > bests > fabio > > > > Dr. Fabio Bernardoni > wiss. Mitarbeiter > > Division of Psychological & Social Medicine and Developmental Neurosciences > > http://secure-web.cisco.com/1dOZP5j8XdDioY7tViTW7NqEi9mrvvba6PAbK6uv63gP7Q8bNrlLCYFkKfvXXNpcvR7MIg3L5wRfoQWO66UdM1HtJA4W7iKqfq4FhnnE9W2R2KwGDIaI7MjIpsOL5VryAdycFZZismV1CFp4rNE47COVEcaN7m-ypDnjnXobdlMmq5EirIKZSBuBmmU3BrEdMYwD-BFb3nS8AdCafRfCfvjcSJaTNtkXlb52Ab49xmqiAfSbLVpAV32A2F_b5QaItKY0wLlYGCGD0ZC1nbr_gag/http%3A%2F%2Fwww.transdenlab.de%2F; > > http://secure-web.cisco.com/1C5zQD6S2aQEn7dMGBOKijRrWY8INlUWuanF5g6gCvX_Y1b1F-tAXUd55vvYP2ExpFYOE4G_Gf0Ujo0hS1Y2GnTUxWS4Q-Hw7ryBf9XfzTCb8akQhMElGzETBV9Y9Dx77zF8x-MJ9GUD0FyloeWVletfQc1s8UEKQ3yoaKTFfJ2V8wWshKFJa_JP1qacQoSHNmMiXI_FcftEAwml4E2oNwVLDD4wbGRONmoBUwVEiXo5dl7kMXPeg0RsJWGcPzoL3tA375bU9hNlgebAeMlJOhg/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm > +49 (0351) 458-5245 > Universit?tsklinikum Carl Gustav Carus > an der Technischen Universit?t Dresden > Anstalt des ?ffentlichen Rechts des Freistaates Sachsen > Fetscherstra?e 74, 01307 Dresden > > http://secure-web.cisco.com/1R3-Q2awQvkHA7pJ5-Bypzc-0X_unyiumlI9PjumZoPxQt07p2OV6Ic1U3XRYL4eNBJal5v0TRUTOvxYTlIeLC1WTMxI-rtEtG8N77JaaMIF13TDkl5R43K7OsP1ahBNt1eNtB_F2H91UBJElxnZ9OxetTmgwCn-WoMBTZsXBsH7BO7zP_6eZ54cIYpYTvBuEgv1DwLFBLnNlUpt_JuYJSDx4zM-kLZt3qrNjw67fNp5cbpAoaJCV0cCgR2NfJCsLdepyT15Wfal__W5aiZ2SPg/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/1R3-Q2awQvkHA7pJ5-Bypzc-0X_unyiumlI9PjumZoPxQt07p2OV6Ic1U3XRYL4eNBJal5v0TRUTOvxYTlIeLC1WTMxI-rtEtG8N77JaaMIF13TDkl5R43K7OsP1ahBNt1eNtB_F2H91UBJElxnZ9OxetTmgwCn-WoMBTZsXBsH7BO7zP_6eZ54cIYpYTvBuEgv1DwLFBLnNlUpt_JuYJSDx4zM-kLZt3qrNjw67fNp5cbpAoaJCV0cCgR2NfJCsLdepyT15Wfal__W5aiZ2SPg/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: Donnerstag, 20. Mai 2021 11:17:05 > An: Freesurfer support list > Betreff: Re: [Freesurfer] memory allocation error > > External Email - Use Caution > > dear Andrew, > > I was allowing 8, 16, ~36GB of memory in different runs, so I would > exclude that this was the problem. > > > bests > fabio > > > > > Dr. Fabio Bernardoni > wiss. Mitarbeiter > > Division of Psychological & Social Medicine and Developmental Neurosciences > > http://secure-web.cisco.com/187My4Jucq7g2iOhroEKk8K8OFGoFoeORTu-mXzokMtuySZfRpdmpBUHAWrZs3PiUgTJQxvI4t7mF19Q65QoVRPm9HIRo1ga6iFYC3emunkTnsx44xyypE8RQ7se9eW1WnrqXrI_Z3OCRQDKjl_O6YrVXw8u2fxs-M2rmDvVwA1c8A6B-TCU2kRIeB7oIt49DW_DM1zE6Vs2u2KvWqA9-ZtIcGYVGPwCKGzShIT5OOvNrJjUldtN0AoNqCDk2gUFd6DjRtozUhmyNbDtaEpIJOQ/http%3A%2F%2Fwww.transdenlab.de%2F; > > http://secure-web.cisco.com/15nLSigNtaEzdHxIpWerC4ukwoFMkkmjnCaSZHFWvxZoHCXH4XhBy49dgkjt_Vq9EFKvYq9xxQ4wmBIAl28GFHwhUJe7IfUAQkVKEMD5fvpyeYO8Shfw1PZr2zy9p7hm86gBaVav8UarY5wXbQ2FUH7lzmO3kgv-sylrFq8rFfmbsx-WSHLLJyi6zQDOV0A7vxj7uJyZDym-vCiDaPrxTdvo7Tws6y8FnBWgAvc-2BMa-GAAkHZJOPrvFuJw9Nh5WXnTa0wo5mD-Qgvp8aHL22A/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm > +49 (0351) 458-5245 > Universit?tsklinikum Carl Gustav Carus > an der Technischen Universit?t Dresden > Anstalt des ?ffentlichen Rechts des Freistaates Sachsen > Fetscherstra?e 74, 01307 Dresden > > http://secure-web.cisco.com/1bhSP0g6m-KCmnhx95IzYxybOAfEOuUmdr5O1AghDUiWJ_SONFEYWrYhfZopDBWkhbc3TWSyW9QsbMRNKTE24SQ_x0a3HOEgV3T4EbIQz1B5mWM6kfZAIiPy36Rhb9HX2U6c3GoyoRPlN7ut_eBPi4d14AvKs_N9pnhWq0dQwrRAHHun-Yqv9qrGkYegJ02POCOw-MnqxRpFSqRpWAOWBZnCq_pGQ2U55zXSRVdQzl3vGgyJxJ3V56k8BwsKP6I8sXGy5TpVmhHFr_P52dATl6A/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/1bhSP0g6m-KCmnhx95IzYxybOAfEOuUmdr5O1AghDUiWJ_SONFEYWrYhfZopDBWkhbc3TWSyW9QsbMRNKTE24SQ_x0a3HOEgV3T4EbIQz1B5mWM6kfZAIiPy36Rhb9HX2U6c3GoyoRPlN7ut_eBPi4d14AvKs_N9pnhWq0dQwrRAHHun-Yqv9qrGkYegJ02POCOw-MnqxRpFSqRpWAOWBZnCq_pGQ2U55zXSRVdQzl3vGgyJxJ3V56k8BwsKP6I8sXGy5TpVmhHFr_P52dATl6A/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 Hoopes, Andrew < > ahoo...@mgh.harvard.edu> > Gesendet: Mittwoch, 19. Mai 2021 20:38:45 > An: Freesurfer support list > Betreff: Re: [Freesurfer] memory allocation error > > Hi Fabio, > > How much memory are you allowing for this process? You might want to just > try increasing the limit on the slurm job to see if that works. > > Best > Andrew > > From: freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bernardoni, Fabio < > fabio.bernard...@uniklinikum-dresden.de> > Date: Tuesday, May 11, 2021 at 4:22 AM > To: freesurfer mailing list <freesurfer@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] memory allocation error > External Email - Use Caution > > Sorry I forgot the attachment. > > > > Dr. Fabio Bernardoni > wiss. Mitarbeiter > > Division of Psychological & Social Medicine and Developmental Neurosciences > > http://secure-web.cisco.com/1UDjtXMiR-HBNL2ou7IruUgW_6SlVjUqDjtbi1gshAUd4B7XmsmBa9Z8UuleJB3EMDmn-chkMz2KAbprcJeE99EZ1oAUuVKqVbsgt5HLyQck6Rwe6z2WVbDws39I6PoQnC1oh3Nq1RFkhVYoLCz85z_gCCWO88hlTppWM88KjtLBVvCJwJLRDgSqDn6W-NaV0klpm8pq5DmW2xbf-u-9cvauFPHaUfgSLWfq5mYKQR3ZQuSQTSifgIeZUlJq8DEka/http%3A%2F%2Fwww.transdenlab.de%2F; > > http://secure-web.cisco.com/15zR6KT49PDBUWwHMuGVVSB1i2ywLodvG7c18nFsxn1WTsFW7yGmn84EQkSAib6vBlG3-sTAqbUriybev9i-Yq9PsVk-FjvLOogqUN_YzOX67Lm6B6n23Vu8LVQ6MK_8C5KhoEJaMoDDu3-jBBxWCkxGI_s2CcqMRfSXlosDaERSb9Kkwk3XqfTLokKrQ6-jgwQqJas_YL-cbRmySD7SuZyXjE3BJD_Z42u6p8yxCxGvWJBBhIlFoMFBex5USw-Wks8tyHl0jiW5JcEKD-ZD3Ew/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm > +49 (0351) 458-5245 > Universit?tsklinikum Carl Gustav Carus > an der Technischen Universit?t Dresden > Anstalt des ?ffentlichen Rechts des Freistaates Sachsen > Fetscherstra?e 74, 01307 Dresden > > http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/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/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/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: Dienstag, 11. Mai 2021 10:20:19 > An: freesurfer mailing list > Betreff: AW: memory allocation error > > Dear Freesurfers, > > when running the longitudinal preprocessing on a subject, I get the same > error as described here (see recon-all.log attached): > > https://secure-web.cisco.com/1my6XFSQF3uEj1ZrgriH6ZF1WxWnqfBMBdiuPDNdXZfq_XO9uhiKwZPYEvG3NS0vJSxZM7hcmTWq1hUXJUt2_XigG_UONfGk8UL_5FWLEktb3qrFvDpcgohhnKOb1j6uAWMIE10PVwXrnLZx4Gf441Olp7jcMNX8eLVVNtPMcFPE5OH3N4cODD6Z83hDSq2HPzZH7tQ78HFekvVecIFyNfG7sKdlEVUVjwFGX6pd4c9fRkVgt6eCj-kuSxbdQrF2OBr2Vi1IX-Bz_UzXD9ZcLyw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg57542.html > > > my FS version is: > recon-all -version > freesurfer-linux-centos7_x86_64-7.1.1-20200714-abaea9e > > and I did not perform any editing, so there is no control points to remove > as suggested in the above post (which also refers to version 6). Therefore, > if I understand correctly, my problem is a different one. Any clue what I > might be doing wrong? > > Other possibly useful information: > uname -a > Linux tauruslogin6.taurus.hrsk.tu-dresden.de 3.10.0-1127.19.1.el7.x86_64 > #1 SMP Tue Aug 11 19:12:04 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux > > > > > Thanks for any hint/help > > Fabio Bernardoni > > > Dr. Fabio Bernardoni > wiss. Mitarbeiter > > Division of Psychological & Social Medicine and Developmental Neurosciences > > http://secure-web.cisco.com/1UDjtXMiR-HBNL2ou7IruUgW_6SlVjUqDjtbi1gshAUd4B7XmsmBa9Z8UuleJB3EMDmn-chkMz2KAbprcJeE99EZ1oAUuVKqVbsgt5HLyQck6Rwe6z2WVbDws39I6PoQnC1oh3Nq1RFkhVYoLCz85z_gCCWO88hlTppWM88KjtLBVvCJwJLRDgSqDn6W-NaV0klpm8pq5DmW2xbf-u-9cvauFPHaUfgSLWfq5mYKQR3ZQuSQTSifgIeZUlJq8DEka/http%3A%2F%2Fwww.transdenlab.de%2F; > > http://secure-web.cisco.com/15zR6KT49PDBUWwHMuGVVSB1i2ywLodvG7c18nFsxn1WTsFW7yGmn84EQkSAib6vBlG3-sTAqbUriybev9i-Yq9PsVk-FjvLOogqUN_YzOX67Lm6B6n23Vu8LVQ6MK_8C5KhoEJaMoDDu3-jBBxWCkxGI_s2CcqMRfSXlosDaERSb9Kkwk3XqfTLokKrQ6-jgwQqJas_YL-cbRmySD7SuZyXjE3BJD_Z42u6p8yxCxGvWJBBhIlFoMFBex5USw-Wks8tyHl0jiW5JcEKD-ZD3Ew/http%3A%2F%2Fwww.uniklinikum-dresden.de%2Fpsm > +49 (0351) 458-5245 > Universit?tsklinikum Carl Gustav Carus > an der Technischen Universit?t Dresden > Anstalt des ?ffentlichen Rechts des Freistaates Sachsen > Fetscherstra?e 74, 01307 Dresden > > http://secure-web.cisco.com/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/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/1lG4Gxlp0lxgj8dZOKjMIUxDkcGck11Kb5W6cyARauBOQGkOXI_zao_xyeyo9-h2nWq3YuUSPcdoiWf1VohymESkdId7Hq7JHCvdYcLcoRHLzCo57EKjAtDpxp1Y1ADlJeGeT9TbNco_pIVOk-WDUYjXvQ3BXWEu4bWIOVndaXXoyQ7XzF115nHBoK4NxmxhFYpu1VhloKCcROKBTjeB51OaH8PkQI6dMCGj_Y6cQ52sIDHMQuZbdm85Pw8wpc0m3hq2UHvAZ61NWFVEQ98MnIw/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/1o1Y3xlwbME1n3aKNjXzGQSIxc55dHM1BEbl1wrgFkE_TFDPgAysargFL54OYEQkzqQuT-idHfxWrjX9JD9cJxuGnzslSgKIYgXPPW7fFxvIlD5RB5gk7Cl57joRtsztgXL76twyZrGWRlN7OGujuX5JZwxmU8bWmhoDRs_gFnwQdmj7Y6onI8JzeAJ7u8BvK84qFrMitHnFpYAXvMxGhfVbneeDNteLH3OvnROuB-WwaFOwNWOflkp7IGYd0ogdtBV47OlIrA_2kjms08imJag/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer > > > > > ------------------------------ > > Message: 5 > Date: Fri, 11 Jun 2021 11:46:23 -0400 > From: Michael Datko <mikeda...@gmail.com> > Subject: [Freesurfer] Issues with recon-all hanging > To: freesurfer <freesurfer@nmr.mgh.harvard.edu> > Cc: "Datko, Michael" <mda...@mgh.harvard.edu>, > stohy...@mgh.harvard.edu > Message-ID: > < > cacdovxezstx7ai5xx3gbkvqw8vgksqobkrklx3h5xeck1+4...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > External Email - Use Caution > > Hello, > > > > I have been collecting data on a 7T scanner, with functional EPI data > collected with 1.5mm voxels, and I have been having an issue with some of > our data where recon-all just hangs after producing only a small amount of > outputs. For instance, it might get to a point where it has generated 5-10 > of the ?lh? left hemisphere outputs in the surf folder, and then appears as > if it continues to run for hours or days but no other outputs get produced > and eventually the process times out and quits. I estimate that this > happens for about 5-10% of the participants we have collected so far. If > it doesn?t work for a particular participant, it will do the same thing > again if I delete their temporary working folder and any outputs and try to > run again from scratch. > > > This is not happening with data from the same participants collected from a > 3T scanner with 3mm EPI voxels, with recon-all run at 2mm. The only > difference is the resolution of the data and therefore the resolution at > which we are running recon-all. Our 7T functional EPI data is collected at > 1.5mm resolution, so for those scans we run recon-all at 1mm resolution. > > > > Do you have any advice for how to get these participant?s data to finish > with recon-all at 1mm? > > > > Thank you, > > > > Mike Datko > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://secure-web.cisco.com/1VokiyVRXNuesJfYu58ovCcqvRbR9u3RL4yM-3CBdOz4qhXN3Uu6EalV3WDv-YmynPDL5f2MEalH7hP9u9FPX6JifdqbmT_hPVAcZ5pjMBZ0jNi96b4jkokirkurO7vraA0MXwxr9MTC7dXdCStXlaJsbcu70YzEAvX8P0D-3k3avaHhpRTSK7TmGp5oW048lpdUmfwrzo-CpPXsupa_TUguPdxFwtMvJfDHdbbvw1UUtelRbmYwq9yJYuz1su5KN9uvazXLZqEnBSy8IhTHv-g/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20210611%2F0cec2ee9%2Fattachment-0001.html > > ------------------------------ > > Message: 6 > Date: Fri, 11 Jun 2021 15:53:38 +0000 > From: "Bernardoni, Fabio" <fabio.bernard...@uniklinikum-dresden.de> > Subject: Re: [Freesurfer] how to visualize statistical maps in FS7.1? > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <233ce09ccbac40a7b3fb34db82438...@uniklinikum-dresden.de> > Content-Type: text/plain; charset="iso-8859-1" > > 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 > Universit?tsklinikum Carl Gustav Carus > an der Technischen Universit?t Dresden > Anstalt des ?ffentlichen Rechts des Freistaates Sachsen > Fetscherstra?e 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 > Universit?tsklinikum Carl Gustav Carus > an der Technischen Universit?t Dresden > Anstalt des ?ffentlichen Rechts des Freistaates Sachsen > Fetscherstra?e 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 > Universit?tsklinikum Carl Gustav Carus > an der Technischen Universit?t Dresden > Anstalt des ?ffentlichen Rechts des Freistaates Sachsen > Fetscherstra?e 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 > > Universit?tsklinikum Carl Gustav Carus > > an der Technischen Universit?t Dresden > > Anstalt des ?ffentlichen Rechts des Freistaates Sachsen > > Fetscherstra?e 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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