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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