Messers Freesurfer developers,

I am using the joint segmentation of thalamic nuclei from T1 scan and DTI, but unfortunately I did not achieve results. 

I installed: Freesurfer 7.4.1, OS Ubuntu 22.04.5 jammy and VM Oracle 7.0.6 r155176.

- Bayesian Tool

Bash:

export TUTORIAL_DATA=/home/vboxuser/SIEMENS

export SUBJECTS_DIR=$TUTORIAL_DATA/GRUPPO_1_6

cd $SUBJECTS_DIR

# Subject's data are stored in subj_01 folder

source $FREESURFER_HOME/SetUpFreeSurfer.sh

export MCRROOT=/usr/local/MATLAB/MATLAB_Runtime/v97

export LD_LIBRARY_PATH=$MCRROOT/runtime/glnxa64:$MCRROOT/bin/glnxa64:$MCRROOT/sys/os/glnxa64:$MCRROOT/sys/opengl/lib/glnxa64:$LD_LIBRARY_PATH

# Run segmentation for subj_01 using the simplified -s option

/home/vboxuser/freesurfer/ThalamicNucleiDTI/linux_x86_64/run_SegmentThalamicNuclei_DTI.sh $MCRROOT -s subj_01

Answer: 

/home/vboxuser/freesurfer/ThalamicNucleiDTI/linux_x86_64/run_SegmentThalamicNuclei_DTI.sh $MCRROOT -s subj_01 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/v97/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v97/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v97/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v97/sys/opengl/lib/glnxa64 THIS IS THE NEW COMPILED VERSION 2====================================================== subj_01, DTI model DSWbeta. ====================================================== ====================================================== Error while running segmentation. Saving error struct. ====================================================== Error using TS_fnc_thalamus_seg_gem_joint (line 250) The value of 'ASEGsharedParamsPath' is invalid. It must satisfy the function: @(x)exist(x,'file'). Error in TS_fnc_jointSegmentationWrapper (line 64) MATLAB:InputParser:ArgumentFailedValidation

-CNN tool

Bash:

CNN segmentation does work, previous steps were performed accurately and without errors.

mri_segment_thalamic_nuclei_dti_cnn --t1 $SUBJECTS_DIR/subj_01/mri/norm.dwispace.mgz --aseg $SUBJECTS_DIR/subj_01/mri/aseg.dwispace.mgz --fa $SUBJECTS_DIR/subj_01/dmri/dtifit_FA.nii.gz --v1 $SUBJECTS_DIR/subj_01/dmri/dtifit_V1.nii.gz --o $SUBJECTS_DIR/subj_01/dmri/segthal.nii.gz --vol $SUBJECTS_DIR/subj_01/dmri/segthal_vol.csv --threads 1

Answer: 

Illegal instruction (core dumped)

How can I do to solve these issues?

Thank you in advance,

Antonio