External Email - Use Caution Dear team and subscribers, I'd like to highlight an issue I've had with recon-all in v8.0.0 and v8.0.0-beta. I've also logged this as a github issue: https://secure-web.cisco.com/1jJPFLQEv-RDDChH3FDSznGS6PwsMf1JbYPxvNx-0gCoDYsVIhE_IPUsOmov_FwsSJYnqPszonW4yFocUKPyTFzsVKnCu36yaSaoSzUaQzXcUSypfRRrhSVGc2nC2Bnftucr18d8B_sbFnnwhSCcb_Ee0aRmyN_GmCZyO0jnGwANH7m2gmx-wk7wsP8KVtzQa5witiGs0lxBjD6GWOo1MiyeJTjJTI2E1ejmTWXQl1ilfzvhbr3jjMPk8hTuQc2rRKvv29rdBDIyZDBNFtKE8uSJnvtYmecPJBcXHDejhRdES5Dsl0Nirn02VDfWMoA73PK1QFDNNl8ZojBIvqOAWTg/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fissues%2F1291
The value of `SegmentedTotalIntraCranialVolume` is always 0.00 . Found out why. It seems the csvprint module needs python2. this has been updated to python3 in commit 9a59bec<https://secure-web.cisco.com/1ye7ehFogBTOSZ5-SI8taauhvvbvu-gHsmX1xAYZrH1X12I0IHDyCUB69jXIwfTtf9ce2xknncGzpF3t6cxmT2wdBFzCb92GyuAIcmrCSIXJDvwd67VBuc1mDDpsXipfpM6vtQlbzUM0osC6LnhgK3xIVaaTClvIWcdnb7MQpbk8wtLukOpWC2GnipgvQbH2ff_4d5bKK2pgxcGNLd2g-pH3ScuO8VU970RmS3WCH308kmJqpomAWSLlKFuI7165zQWv6K-yT350Fz1B3qpL5QIbb6oATxwPGwGd2U5OS6AWuUteCSUTeOCM723aU4oFmepZuQJo4R4VYCOBJg4JDPA/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fcommit%2F9a59bec7e01d3ae14a692a57cb2547d9ed72c920>. However this commit did not make it into the v8.0.0 or v8.0.0-beta version <https://secure-web.cisco.com/1ye7ehFogBTOSZ5-SI8taauhvvbvu-gHsmX1xAYZrH1X12I0IHDyCUB69jXIwfTtf9ce2xknncGzpF3t6cxmT2wdBFzCb92GyuAIcmrCSIXJDvwd67VBuc1mDDpsXipfpM6vtQlbzUM0osC6LnhgK3xIVaaTClvIWcdnb7MQpbk8wtLukOpWC2GnipgvQbH2ff_4d5bKK2pgxcGNLd2g-pH3ScuO8VU970RmS3WCH308kmJqpomAWSLlKFuI7165zQWv6K-yT350Fz1B3qpL5QIbb6oATxwPGwGd2U5OS6AWuUteCSUTeOCM723aU4oFmepZuQJo4R4VYCOBJg4JDPA/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fcommit%2F9a59bec7e01d3ae14a692a57cb2547d9ed72c920> It seems that the -motioncor step in autorecon1 in recon-all prints the value of Total Intracranial Volume from the mri/synthseg.vol.csv into the text file stats/synthseg.tiv.dat. This file is read by mri_segstats later in the process to make the aseg.stats file. When csvprint is broken, the file stats/synthseg.tiv.dat is empty, so the value of SegmentedTotalIntraCranialVol is 0 in aseg.stats. I believe this should be logged as a known issue for these software versions because the software incorrectly reports the value of sTIV in aseg.stats. A hacky temporary fix would be to copy the csvprint python file from the mentioned commit, and overwrite the version in one's freesurfer install at $FREESURFER_HOME/bin/csvprint Abhishek Roy, Oxford Brain Diagnostics.
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