External Email - Use Caution many thanks, Henry, that's super helpful. Btw, I came across the segmentThalamicNuclei_DTI.sh here ( https://secure-web.cisco.com/1E9W0mtw7h6DQWHzDJCtjIVC4xULq9MtdNdnPuNoniqHdjaZ2ynk8j07eI8tubOCGcJBcf6N3rdj1lrBJt-HDOOhrFirmrL0QarM7lX0jIm-QtBT7U5smu5tkilMiQIkK_0UySRCAuEwpt0uHQppVPCNeamIrJR-TcfHN_Qt6th2bMrahi5LjQqkv2TJX8q8Io9ML3dbaxUN3jEjycvTwP9KpiSDm7LaAdbJr41C5qKg677La49_PWOAsxZQAViC_t_A2AgTVC8NEOt3iqQDrDITiFwcytpPyO_xFmCrCqzbyiNUUeLuY_83poTDrqLzrkYsm5FVjgj0ZAojJy2vuuw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2Fdev_binaries%2Fcentos7_x86_64%2F%3FC%3DM%3BO%3DD). am I right in thinking that your Bayesian module is now integrated into the Python framework? No worries if not, obvs, can't wait to run it, I guess ! :)
many thanks again g On Fri, Apr 12, 2024 at 10:59 AM Tregidgo, Henry <h.tregi...@ucl.ac.uk> wrote: > No problem Georgios, > > > > It’s easily done. I’ll check if we can streamline the patching process. > > > > I’ve written a bit of an explanation below in case you or anyone else on > the freesurfer list comes across a problem like this again. > > > > Best wishes, > > Henry > > > > =========================== > > > > Explanation: > > Many of the network-based tools in freesurfer are distributed as python > scripts which build a tensorflow or pytorch network, load the model weights > from $FREESURFER_HOME/models and push the data through. As changing the > combination of python package versions can have unexpected effects, > freesurfer comes with its own python environment “fspython”. For these > python-based tools the files in $FREESURFER_HOME/bin are shell scripts that > run some checks then pass the python scripts in > $FREESURFER_HOME/python/scritps and any arguments to the fspython > environment. > > > > In this case replacing the file in the bin directory with the python code > likely meant it was running in your local python environment using > different package versions. A clue to this is the deprecation warning > mentioning numpy version 1.25 as the version in fspython is 1.24.3 > > > > *From: *Georgios Argyropoulos <gargyropou...@gmail.com> > *Date: *Thursday, 11 April 2024 at 17:24 > *To: *freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>, > Tregidgo, Henry <h.tregi...@ucl.ac.uk> > *Subject: *Re: [Freesurfer] Question on using thalseg_1.1.h5 > > ⚠ Caution: External sender > > > > Many thanks and apologies, Henry - I figured it out... I stupidly replaced > your improved segmentation script in both the scripts and the bin directory > instead of only replacing the former. > > > > many thanks for your time, much appreciated > > > > g > -- Georgios P. D. Argyropoulos PhD, CPsychol, FHEA Division of Psychology, Faculty of Natural Sciences; University of Stirling; FK9 4LA Scotland UK *Personal Website <https://secure-web.cisco.com/1vBM_j8UN7Hi5FY6pwPi1zUPGObPH-pid1nOPdKDajWFgWLa5axEkqch7ljVN9p2MUgjlOUUtEpuoOLofawcsjQhNARcBrrHrqceRcHCsgY597wYX1l0nnT0PsBwDMKK0mUc88CwQxCQxsnFuZujmUFrBF_dRqEncmPk9leiharuA9fhuEsw422HRrdSLWTiv-YvtUY6b3QVzyL7uW1WQU9KQ_ordq1inqdqTAVB5y0cWil2mX_eVeNPJO9XlYNNNvb1XLTpCrJEM8v1yyCs2EMJavuhdiAg24saCzRzAL8DiBrFw4ei-10R_hHVVe3Oi-sw-3nH2K_H8mqvdnasemA/https%3A%2F%2Fsites.google.com%2Fview%2Fg-p-d-argyropoulos>*
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . 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.
