Hello,
can you tar up the model_<struc>.txt files, mist_filenames,mist_subjects and two subject folders and upload them to:
https://oxfile.ox.ac.uk/oxfile/work/extBox?id=700839B35190E48BF
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
> On 20 Feb 2018, at 02:39, Sudhanshu Manda <[log in to unmask]> wrote:
>
> 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
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