External Email - Use Caution 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/10fYYXOWWjqutAb_GMihL-D_9qeFb384gjm8TyyMhafr_1SIDQL5bcGAspJvI4DoyopzjmIInUv2RWHzyZCrR1k7n2_swBNC32bBKpJ8kgSnmi73OCwXARWN94ax6w42QvvfQdYyTFheIdH8kBIVtKbleVOdQSO0aEUOPsLzcm2XqipuoDDPSPjm2XGcpw7h_vocNP_-Szdp2os9wN79hEVnctlIUosSOcOSmcfDJO4LfOUV0qx69E06JlqCbzOASJxEsNyf8HLIcIf1NnPhj6ZCI4JJIpZL-iy-OOqU1NdFXCdaVO-VWvDjljtayJF8YPB6-nvoxxY7Arcx_Pw1nAA/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/1cK7n5ASIB0kkfSRgetRobamJixmzgB67pjDT9skthB0s8vN5a1JDhpmFwRLuigN1usk71O25Ycr7ZXd7NoDAum7eorx4XXRwffvbLUIuDLmPkBBkt6LflsVJXrS9X9vDGefOhw5R9pHQZhKcyuZrUTN-pZKvGEuOIhcnwJcFzus9wmR8v4XykML4bp5-OOaoLturv6Xx2XLjdJJA5KY5iOdQ-6HZFfHW6-UJSfH59jHMQyo0c2IAWmNZcHMr1eqCDX5tXSKNmx9sy0k413nNtzYVXQx0zNMyHCONtF_J53bgDoomYl_FJ62tTLoV-ZgOB-2j6sKr-a5lBW3xw0nnDA/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/1cK7n5ASIB0kkfSRgetRobamJixmzgB67pjDT9skthB0s8vN5a1JDhpmFwRLuigN1usk71O25Ycr7ZXd7NoDAum7eorx4XXRwffvbLUIuDLmPkBBkt6LflsVJXrS9X9vDGefOhw5R9pHQZhKcyuZrUTN-pZKvGEuOIhcnwJcFzus9wmR8v4XykML4bp5-OOaoLturv6Xx2XLjdJJA5KY5iOdQ-6HZFfHW6-UJSfH59jHMQyo0c2IAWmNZcHMr1eqCDX5tXSKNmx9sy0k413nNtzYVXQx0zNMyHCONtF_J53bgDoomYl_FJ62tTLoV-ZgOB-2j6sKr-a5lBW3xw0nnDA/https%3A%2F%2Fsites.google.com%2Fview%2Fg-p-d-argyropoulos>*
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