anagrammarian/thomasmerged repository overview

This is the old container of HIPS THOMAS we are maintaining for historicity and for people to recheck analysis etc. We recommend you pull and use the latest container which is here https://hub.docker.com/r/anagrammarian/sthomas⁠

The help for this old container in detail can be found here https://github.com/thalamicseg/hipsthomasdocker/tree/v1.5⁠

To run HIPS-THOMAS, each anatomical file should be in a separate directory. You can launch the container from the command line by running the following command inside the directory containing the T1 file (I have called it T1.nii.gz here as an example)

docker run -v ${PWD}:${PWD} -w ${PWD} --user $(id -u):$(id -g) --rm -t anagrammarian/thomasmerged bash -c "hipsthomas_csh -i T1.nii.gz -t1"

The -t1 option causes HIPS processing to be done before running THOMAS. HIPS synthesizes WMn-MPRAGE like images from T1 data improving thalamic contrast and also allowing standard THOMAS to be run which uses CC metric for nonlinear registration and joint fusion. This is not possible with direct T1 as the contrast is different from the template and forcing MI metric which is less accurate and majority voting for label fusion which is also suboptimal.

This container can be used to process WMn MPRAGE (FGATIR) data which is where it works best due to the better intra thalamic contrast. Here WMn.nii.gz is the white matter nulled MPRAGE file (or FGATIR if you will/must).

docker run -v ${PWD}:${PWD} -w ${PWD} --user $(id -u):$(id -g) --rm -t anagrammarian/thomasmerged bash -c "hipsthomas_csh -i WMn.nii.gz"

Note the lack of -t1 option as HIPS is not needed.

For wrapper scripts, batch, qc etc, please check the docker site https://github.com/thalamicseg/hipsthomasdocker⁠ (thomaswmn and thomast1_hips are the 2 wrappers)

Singularity: You can directly pull from dockerhub and save as an sif file. First install apptainer from here https://apptainer.org/docs/user/main/quick_start.html⁠. Then run singularity pull thomas.sif docker://anagrammarian/thomasmerged

You need to tweak the calls slightly from docker usage below but briefly for T1 run the following: singularity run -B ${PWD}:${PWD} -W ${PWD} -u --cleanenv /path/to/thomas.sif bash -c "hipsthomas_csh -i T1.nii.gz -t1 -big"

For WMn/FGATIR run the following: singularity run -B ${PWD}:${PWD} -W ${PWD} -u --cleanenv /path/to/thomas.sif bash -c "hipsthomas_csh -i WMn.nii.gz "

Note that the thomas.sif can be saved anywhere and that is specified in /path/to/thomas.sif which will be replaced by /home/yourusername/bin/thomas.sif if you save in ~/bin for example.