External Email - Use Caution Hi Henry,
hope you're well. Here's the preprint we've prepared, acknowledging your helpful advice. https://secure-web.cisco.com/14kZPt7OhtlrZeaQh7Ew8aG5CEUsAlZfjqzmCWTY-C8ekRNu9dFUq3z8qS35PqC5Q046EToELogkMGUaxNYDkWyMTyE_4PEC6wbXBAFAlnWuNy_7KcdCqA5LsD1QcbNZt74QS-CQSD9hBP7zmo6rEWDTBLIi8CGS_pGe0d4XcvEvJaOXsWpfz6fhSAGkAilchmYD_BvVnDvsM2DQk_LGsXoAVet8ot23ukoNftq_t1LeN6GW8BniBy7chlUWgDu-1_egnwaoxCo-mCLq8q0jgMtVACptD7ilRd0m0AnaFCzwMJ8x8yTZ_zDa1dmSwyAkg/https%3A%2F%2Fwww.biorxiv.org%2Fcontent%2F10.1101%2F2025.05.21.655297v1 Don't hesitate to let me know if you'd rather I didn't, or if you come across anything that's just utterly wrong! many thanks again georgios On Fri, Apr 12, 2024 at 11:49 AM Georgios Argyropoulos < gargyropou...@gmail.com> wrote: > ah, gotcha - many thanks, Henry, much appreciated > g > > On Fri, Apr 12, 2024 at 11:19 AM Tregidgo, Henry <h.tregi...@ucl.ac.uk> > wrote: > >> The Bayesian code is in the development version of Freesurfer yes. >> >> >> >> At the moment this is the original compiled Matlab code used in >> development of the algorithm. Running this requires a matlab runtime >> similar to the original segmentThalamicNuclei.sh script from Freesurfer >> 7.0. We have someone working to integrate it into the same python framework >> as SAMSEG and segment_subfields but we are limited by available developer >> time. >> >> >> >> BW, >> >> Henry >> >> >> >> *From: *Georgios Argyropoulos <gargyropou...@gmail.com> >> *Date: *Friday, 12 April 2024 at 11:04 >> *To: *Tregidgo, Henry <h.tregi...@ucl.ac.uk> >> *Cc: *freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu> >> *Subject: *Re: [Freesurfer] Question on using thalseg_1.1.h5 >> >> many thanks, Henry, that's super helpful. Btw, I came across the >> segmentThalamicNuclei_DTI.sh here ( >> https://secure-web.cisco.com/11fx38DfaOfTS3qRt2fPblgzLzQSaJ7x10NPQ2KQYHFPTTiu2Y1Lsd4Y0wP03Yf5_Ilih9MlQyyBR4z33fIxYidlrKiRFsa4kwjA2vlhmIJY2E4Wex9kiopPdl7bbYxWJ0Qf_TNJfz3YFgup73Gz3n7_XWl8jQ_EVtgY5uC7-qEmc8lUdmEjAwiYocXeNLMYUgUz7OLWOydM6sE9HOEIqgVFvCZ9aYTueurLQAdpeynoxQCcbYC__4WVoE1dwphjHJ9hcRtSHE7y8Wf8dMgtB1NnAtgHUJ6d3A1feaOQ2AlqBIX8E0SUKV8OkQ5Lp6px5/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/1HTezobC3shGWnJ4DLwpfJNcyOcLPLN2FJDWGKovU_N9AYjffM8xqEnrfiABcdpj3Gf_uH6tZ6AwV9VPkKDRNwrzAAlSLRWkgc5BUr3XvpMuJrcRpRYfxWWiyTcEdoZlpjodopJ53B4vVXAXY_6f0FBAVz3disX_TbF4yAHhbP20JvA62xuH3mVr1v8YcQK2RhF7QeW9Ud87XSQfeAZOQ0gA5KCvi3PSiiKE4FpZ2h6O1pD6cZqc24CBacittT8k3yjIPL1rMwU68sT72MMvEnRbKAkBixkuS173mxFWSav2N3GlbSEu59oEFTZtskzzJ/https%3A%2F%2Fsites.google.com%2Fview%2Fg-p-d-argyropoulos>* >> >> > > -- > 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/1HTezobC3shGWnJ4DLwpfJNcyOcLPLN2FJDWGKovU_N9AYjffM8xqEnrfiABcdpj3Gf_uH6tZ6AwV9VPkKDRNwrzAAlSLRWkgc5BUr3XvpMuJrcRpRYfxWWiyTcEdoZlpjodopJ53B4vVXAXY_6f0FBAVz3disX_TbF4yAHhbP20JvA62xuH3mVr1v8YcQK2RhF7QeW9Ud87XSQfeAZOQ0gA5KCvi3PSiiKE4FpZ2h6O1pD6cZqc24CBacittT8k3yjIPL1rMwU68sT72MMvEnRbKAkBixkuS173mxFWSav2N3GlbSEu59oEFTZtskzzJ/https%3A%2F%2Fsites.google.com%2Fview%2Fg-p-d-argyropoulos>* > -- 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/1HTezobC3shGWnJ4DLwpfJNcyOcLPLN2FJDWGKovU_N9AYjffM8xqEnrfiABcdpj3Gf_uH6tZ6AwV9VPkKDRNwrzAAlSLRWkgc5BUr3XvpMuJrcRpRYfxWWiyTcEdoZlpjodopJ53B4vVXAXY_6f0FBAVz3disX_TbF4yAHhbP20JvA62xuH3mVr1v8YcQK2RhF7QeW9Ud87XSQfeAZOQ0gA5KCvi3PSiiKE4FpZ2h6O1pD6cZqc24CBacittT8k3yjIPL1rMwU68sT72MMvEnRbKAkBixkuS173mxFWSav2N3GlbSEu59oEFTZtskzzJ/https%3A%2F%2Fsites.google.com%2Fview%2Fg-p-d-argyropoulos>*
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