External Email - Use Caution Hi all,
I have the same issue on Ubuntu 22.04, patch is installed. Many thanks, Yann > On 20 Dec 2022, at 04:29, daedalu...@aol.com wrote: > > External Email - Use Caution > > > Dear FreeSurfer Developers, > > We are interested in implementing " mri_sclimbic_seg " from FreeSurfer 7.3.2 > and are having trouble getting it to finish processing. > > When I tried to run mri_sclimbic_seg. I keep getting a python error and the > process never finishes. I searched through the forum and it said that this > was a known error and that there was a patch. When I installed the patch I > got the exact same error. > > The error message is: “ValueError: operands could not be broadcast together > with shapes (4,) (3,)” > The link to the forum post is: > MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" > claiming to be > https://secure-web.cisco.com/1AOO2G3Y9tIa3C9R7SheXdTmfFlIb7ZE6S7sOyW05Pn5KgUixvaLbdD9R1S6_Zi3KZjHAxNtpCZE3cPPjsACbaj0MP4zQqxSVGDRjTV8yfBtix-5EBxDDM_u2DGLzEPfKHNrV4jtEvpXA7sKFoxeMQ8XnpvNXlnaNbUityY1bkGrb7RK49FccouDavh7x8l2DNWz-w00BObPqu2ZP7CSfM5W5DffZk5ZiDpMH8GCh_WApOI6SwGuqz90fE2YtOFT2hjq3BMCI6Uyut8rMbXgLh38CxtmF5PXbBQREWN6aF5kqZFfB05KyviFvQALJWJ-Tl_T1E6eUQAgjiJv1_Ws3eg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg73652.html > > <https://secure-web.cisco.com/1BI_B41UWHwWJM3wQhzsqKLiN64Mdzk_AasgGunt7xAFi2Ti_IjaFqr8pVIuvUSD-ZLVEYI580vCnKVFO3EYgxKHmRJ2JwpJgt3IrlnVqXehDvlnA8m_QLcspvwOdEyuleG-SRP1hVpkuenwO4m4bfOK032XeTJ-p-yONPUHX8tZqDwR92JwPKU0O4ndK6mrXvnLvHl5tb0-tWBv59QOli-_OgfEo4ussU6uuv1voORx52Y1Cv4lPDV1kOknbYt_fapRm5e5mIgyQlFZfvQH2LXhv8ygBuozck_eNWt6s8tElJMnagVvzHCElOjzFYRnL_c_5eZh4VSDBJvRl1YwX7Q/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg73652.html> > > We tried running it on the test subject “bert” just to make sure the issue is > not with our test scan and I got the same error. > > We are getting the error even after installing the patch. Here are the > details of the command line I used to run it and the error message: > > Command line: > mri_sclimbic_seg --s bert --o > /usr/local/freesurfer/7.3.2-1/subjects/bert/mri/mri_sclimbic_seg.mgz > --write_volumes --write_qa_stat > > Error: > Traceback (most recent call last): > File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line > 1049, in <module> > main() > File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line > 232, in main > segmenter.process_files(**params) > File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line > 578, in process_files > post, seg, vox_counts, volumes, mean_probs = self.segment(image) > File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line > 498, in segment > conformed = self.preprocess(image) > File "/usr/local/freesurfer/7.3.2-1/python/scripts/mri_sclimbic_seg", line > 490, in preprocess > processed = image.conform(shape=(*self.inshape, self.nchannels), > voxsize=1.0, orientation='RAS', dtype='float32', copy=False) > File > "/usr/local/freesurfer/7.3.2-1/python/lib/python3.8/site-packages/surfa/image/framed.py", > line 574, in conform > conformed = conformed.reshape(shape, copy=False) > File > "/usr/local/freesurfer/7.3.2-1/python/lib/python3.8/site-packages/surfa/image/framed.py", > line 515, in reshape > delta = (np.array(shape) - np.array(self.baseshape)) / 2 > ValueError: operands could not be broadcast together with shapes (4,) (3,) > > > We are beginning to study professional and amateur fighters, and we suspect > that shearing/disruptions to the septum pellucidum may have downstream > consequences to the connectivity/DTI measures in the septal nuclei, mammilary > bodies, etc. > > Thanks in advance for any help or comments you can provide. > > Sincerely > > -Randy > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1xm9U-U9fxPeniR-eyucnOvn2u9TwQEw0fizLmts2HAtkaVN17yZgm584LLSXBtrGux8M3J6VCtuw7sq5Q-gJ_3FJnbyz8LQy9oqwXE2pSQMnlbpGtAoqRDJYK7VRgcVdssLPoHQcu5ihs-6lDiumckgriHbu58t-1PH0UVKqPOdRT8f7nXtE3pmoK9vJDIbUlQUb6Vd122lrtmAENXzRZXDQ8K5PlTUpbcBJMwGfsRSPd7cBlQFFl1N39pfxWY9gpZ3P6ohxO2ffTWsL16qvQGYx7D2Bw8e_dnG5bmxhFLn2hBtkEYxS7aluxkimhFwuvYUvlqFRPqVz1ODgO6X-ZQ/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 > https://secure-web.cisco.com/1qgz4kgBXfgANC7q4_rIIhlCtGxv9lmKbUgHtHh92EToQgZRk2Jp5SsI1SkC9T_rVk-a1Duen0CvXVx7gUWMI5YmBKVHu_yRkJk0xuSy481rCAOvWLE2_hFWgQOsWSjmS1a0YLZI6sDy8QcsA1RF6uIWFdBScFCsrMq8K_Q-ru1pZ8Fj9nTA_ei_M4ifmGJRm_NIhcSOOehcBBEHF7JAQlAXZCGllKrrwxuadV0A52kceKbK8rcN0uglNcYcFnm6TRMuuwrxs4GfugvCXoTtjL2xb5KW2sx1-emAhu9CJrZi5nxNdIemX4GSNXncPmp3IxOXw4mmG2TTUfGGyKPONBw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline > > <https://secure-web.cisco.com/1qgz4kgBXfgANC7q4_rIIhlCtGxv9lmKbUgHtHh92EToQgZRk2Jp5SsI1SkC9T_rVk-a1Duen0CvXVx7gUWMI5YmBKVHu_yRkJk0xuSy481rCAOvWLE2_hFWgQOsWSjmS1a0YLZI6sDy8QcsA1RF6uIWFdBScFCsrMq8K_Q-ru1pZ8Fj9nTA_ei_M4ifmGJRm_NIhcSOOehcBBEHF7JAQlAXZCGllKrrwxuadV0A52kceKbK8rcN0uglNcYcFnm6TRMuuwrxs4GfugvCXoTtjL2xb5KW2sx1-emAhu9CJrZi5nxNdIemX4GSNXncPmp3IxOXw4mmG2TTUfGGyKPONBw/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline> > .
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