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Hello, I wanted to continue off my previous thread because the issue has still not been resolved. While I am able to run mist_1_train successfully and create 'model_<structure>.txt' files in the 'mist_out' folder, I am not able to run mist_2_fit successfully and output segmented subject images. My folder structure is: .../studyfolder/mist_filenames with syntax per the MIST User Guide. Let's assume the .NII.GZ files referenced are file1.nii.gz and file2.nii.gz .../studyfolder/mist_subjects with a list of subject subdirectories .../studyfolder/subject1/file1.nii.gz .../studyfolder/subject1/file2.nii.gz .... same folder structure for other subjects... I have put a valid directory name in 'mist_subjects' that points to a sub-directory from where I run 'mist_2_fit' that holds the nii.gz files called for in 'mist_subjects'. The output of 'mist_2_fit', according to the MIST User Guide on FSL (link below), should be: "... mist_<structure>_mask.nii.gz. The final segmentation as a voxel-based mask. mist_<structure>_shape.mim. A mesh representing the final segmentation. This can be used for shape analysis (see below). mist_<structure>_shape_reg.mim. The same mesh after affine registration to MNI coordinates. This can also be used for shape analysis ..." However, after running 'mist_2_fit', only the following files were present in my directory: mist_t1_brain_mixeltype.nii.gz mist_t1_brain_to_mni.mat mist_t1_brain.nii.gz mist_t1_to_mni_nonlin.nii.gz mist_t1_brain_pve_0.nii.gz mist_t1_brain_pve_1.nii.gz mist_t1_brain_pve_2.nii.gz mist_t1_to_mni_warp_inv.nii.gz mist_t1_to_mni_warp.nii.gz At first I assumed this was just intermediate files and that the program was still running. However, it has been quite some time since, and I do not think the program is running anymore. Therefore, I'm not sure of the purpose of these files. Does anyone know what these files represent? Is there an issue that I'm missing that's preventing me from getting the correct output given on the FSL website? Thanks! FSL Link: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MIST/UserGuide