External Email - Use Caution Hi Yujing,
I followed the instructions in the release notes. https://secure-web.cisco.com/1CdxIQH0irUTxU0_ASr2OXmiW1p1iEZNtk_XgyrahH6JLBn0o43pAf5fzJCTWqTPjvkGvVdCuyKCaMOhShEgGXwS-Yn2XWhxiooFTIeeXgUU4tLBx0DzlVvgDJ5zGJlfREDn0aUhPYnRObXatz4un16k7Skzwhd5qYNbc3dHKgyH4MK--B98Wk9ON2hokvLGxhqrwHbopswU9IcC6amjWIY5eeHt8Vj8zbBvPN-mMqVhnDD8zb9YNxVBKj8AFbDtxZGD_BO0-nIKfkk69Ix1QFgVvuw8j7qAcI0mI5LA6ygZ1CXHc6-vMTF7b7dH05nnZ3wWySDBxkp-adZWLphO4UA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all-clinical * Please replace $FREESURFER_HOME/bin/recon-all-clinical.sh with the latest version HERE <https://secure-web.cisco.com/1P3JN6CBNHomG3q-lM4hcusxhcgVFkFalyz0XoR77Qh8DW1umcKXa_j8dcSWuWLszSR2mo-izKg3fyQ4cFLm8GJFN9-onxczbUk2SxGT-FXdQ0jJ3xzSVjL7mS3Rkkb2IRw94FLNUKXvdWccFpHkk1FAxIt0HVCmxYOMLbyU0nU2AR_w0ZZEJJ8E9V7Mu4NlGJXRY0k6fvDe1FwOISKNG9mbJlv2lFVYyQXJMKZy-2PUEjBWk2-uwQPwGP5ThP3QULTqwp8BwYhZbjFpTuj3QKT6grS-F3XA4lEdg6-XZkFspE_hN2OQdD4W5Lma2rYzfKDKj7NDc-2iBWw5ozKlziQ/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Frecon_all_clinical%2Frecon-all-clinical.sh>. Development versions newer than June 15th 2023 do not have this problem.]* The original errors went away but new errors came because the colortable_BA_thresh file was missing. It took a bit of detective work to figure out what was causing the error. Maybe you could change the release notes to tell us what the correct fix is? Michael On Tue, Jun 27, 2023 at 3:06 PM Huang, Yujing <yhuan...@mgh.harvard.edu> wrote: > External Email - Use Caution > > recon-all-clinical.sh in 7.4.0 and 7.4.1 should not be referring to > colortable_BA_thresh.txt. The changes should be only available in dev > version of Freesurfer to fix issues mentioned in this posting *MailScanner > has detected a possible fraud attempt from "secure-web.cisco.com" claiming > to be* > https://secure-web.cisco.com/1X_197AYIYOLIUYIl_EhLe_m2AOUi0UvLwJNVuIWlNlrNwbASOOa3wYqyL_OUk6QCqJNTQ9KcNuDsestCnwoX_WOETRwD4FeRORCZeQMA0yJc380vk0D2UPcQLPWgRBJcjDXLlofqYhlJu9ZbWz4kCStLiLnHLD2nMSWuEtQqhD0p7LJAMo8FveyrBj5PNTktfYLefm6Ik5lJbXSDCTdUWdoMNB0UDolxBLyDHGIfur8XZQytP3mjK9ILy_kHYK4MxZHcoNIoDW7iYFJFHiAMRCOF2QkYgqLCbWOy2qDCoP5EBd8n33BFjqBiIIgHQLukQdac033XWGZiPwc6FdMDhA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg75079.html > <https://secure-web.cisco.com/1ZoBhZ0yodRMjWWo95EEpJf_-_vZXGIXM5fmA4K6OMvAhUVD7p0dApttlxzW_KFJYsEnsQnQUIfcCjaMZjT_kUtarbKPGQK0PUJ9xrKzeMuD6E-Ipr-RfmS9txeQvjhE8PzVSVvP75X2L3NRM_VItiJYeeZzscOChLZd1tlI6bzqpGGPzWGLHrU39amHdLvhfrFpkz8lfX8sRFNcPpp2XBZ_QwzUzClet555INGoarmq3jSGCA_jL7JyTcqSSPjsqU-o7uyYTW7Sp0UT6l9ledw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg75079.html> > > > > You can use mri_segstats (*MailScanner has detected a possible fraud > attempt from "secure-web.cisco.com" claiming to be* > https://secure-web.cisco.com/1a17RmyhauaB9mFSA6aprXldSg_-2-39P5FYvg7hfl8t49aMP2DFGMLiO5pQzJ-DVHVt0Hoygl7ccZFnabWDxKSMS0Rq52kX_w9dxA9tOnk6nB4c-OJJFwtc43NOkferTAO1UpCShNtj_L_pMltan1R3IbjKBbTdB_7dqtv2vZfFENlCitPm3wAVJzt3GABxUza2TCmxBix6UwTqpYq35veoCcGRCjgoBfWFHCwrdqcrEimEHtpMStUgFurLAVe0HbpAV6D9L6HsaYUa62Cy22qzlyKYevrFyYhylzZRlILVMQLur-x457AbHx2BqxUig4JadVfJ7F2T_tjqatmmGhw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_segstats > <https://secure-web.cisco.com/1teY49SYvCW3T6R6fhT7LaRGqaJw378vDsUp4c1cjPxJhqboeZ96lnw8668czbRDm3B8b7DhXe4poGzHiUmIHYt3Avuy7ot4de9FZVcXGGJQJ51uiejkqvdcaO2fYPMwomnCvleirgOc97nSiUqmRK8-hea2dE_2u0qvLruzW8nQAPt1X94caURvtwZlCZ9wb5IcNoYhixkMpHPku923OSIHwGL0eYtVgIf5u8Z-zEpQdlZjLI2qv30XTCGErW196iJ3N-7D_nkhOafIxoTPFxQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmri_segstats>) > to generate the missing stats/aseg.stats. > > > > Yujing > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Michael Mc Laughlin > *Sent:* Tuesday, June 27, 2023 8:23 AM > *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > *Subject:* [Freesurfer] Missing file colortable_BA_thresh.txt for > recon-all-clinical > > > > * External Email - Use Caution * > > I finally was able to run recon-all-clinical.sh without errors! > > > > There is a file in the development fork on Github called > *colortable_BA_thresh.txt* in the *average* directory that is not present > in the 7.4.1 release. When I downloaded this and put it into the 7.4.1 > release, the replacement recon-all-clinical.sh ran without any errors. > > > > I also solved the mystery of the missing lateral ventricles. The file > mri/brainmsk.mgz in the clinical version is a synthetic file that doesn't > contain any ventricles. The equivalent to brainmsk.mgz in the clinical > version is synthSR.mgz. This has the missing ventricles and indeed all the > other brain components like the cerebellum etc. > > > > Alas, despite running error free, there is still no stats/aseg.stats file. > I hope that this is on the TODO list for the developers. In the meantime I > will write a matlab function to extract the aseg stats from mri/aseg.mgz, > which seems to have all the necessary data. If anyone wants a copy of this > please email me. > > > > Michael McLaughlin, > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1tvaq9Bw2aIr2fAMxxcH4pA4KAARZYyMT7qUkJJqrPc3LaTuT0DziNwR4U0ao3bQCCmQxBEq0NtAZryyGQ5F0Obp_sgUjxaILYxh44Pbb0hJI-cpDy_dlvQdu25Oj7v_sNecRqBPlcjOXdq9cA59edEKTt76VyN7MmacNLrID8g8Hj5prFcaaMx8qN_VFR-CLZup-a_nTvhjfgx8l9i_1tEZ6evA9CspD2oiO7yg3Qz-hQ7Qw0owBUwMuf5RS_8HocWzkghS4RqzJF2H8_r7VFRJcPiZNfXmwKT1szNJ6yWzIt8gvXmFF0bVSbu3vz2GmPunWLrVvIGWL-8W7Uysg7g/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. 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