uxhao/dwitool repository overview

⁠dwitool

Author: uxhao ([email protected]⁠)

⁠1. Description

dwitool is a pre-processing and analysis environment for diffusion-weighted imaging (DWI) and magnetic resonance imaging (MRI). Built on Ubuntu 20.04, it supports CUDA 11.6 and CUDNN 8. It comes pre-installed with a VNC service that provides a minimal desktop environment for the convenient use of various neuroimaging analysis software viewers. Additionally, Miniconda3 is installed as the Python environment manager.

⁠2. List of Pre-installed Software

• FSL 6.0.18~19
• FreeSurfer 7.4.1
• MRtrix 3.0.8
• MRtrix3Tissue-3Tissue v5.2.9
• Ants 2.6.3

and others:

• SSH
• VNC (providing GUI service for viewer of neuroimaging analysis tool, such as fsleyes, freeview, mrview)

⁠3. Usage

You can use the ssh tool like Xshell connected it via username(root) and password(root). If you customized the username and password when you created the instance, log in according to your settings.

for ssh, 127.0.0.1:6000
username: root
passwd: root

If you want to use GUI viewer of neuroimaging analysis tool, you need to install TightVNC Viewer⁠.

• for 64 bit you can click here⁠ to download TightVNC Viewer.
• for 32 bit you can click here⁠ to download TightVNC Viewer.

You need input 127.0.0.1:7777 into the input box named Remote Host in TightVNC Viewer, and then click Connect. Then you'll see a black screen. At this point, simply right-click anywhere in the window to reveal the Terminal emulator option. Clicking it will open a terminal window where you can enter commands for any viewer.

**Note: **

• The 7777 in 127.0.0.1:7777 refers to the port you mapped when creating the instance to connect the VNC service (5925) inside the Docker container to your local host machine.
• If you want use Nipype, you should pay attention to that there is a bug in nipype.interfaces.fsl.preprocess.py.

# modify line 936-944 in /opt/miniconda3/envs/xxxx/lib/python3.12/site-packages/nipype/interfaces/fsl/preprocess.py 
        if isdefined(self.inputs.mean_vol) and self.inputs.mean_vol:
            #if LooseVersion(Info.version()) < LooseVersion("6.0.0"):
            #    # FSL <6.0 outputs have .nii.gz_mean_img.nii.gz as extension
            #    outputs["mean_img"] = self._gen_fname(
            #        outputs["out_file"] + "_mean_reg.ext", cwd=output_dir
            #    )
            #else:
            #    outputs["mean_img"] = self._gen_fname(
            #        outputs["out_file"], suffix="_mean_reg", cwd=output_dir
            #    )
            if op.exists(self._gen_fname(outputs["out_file"] + "_mean_reg.ext", cwd=output_dir)):
                outputs["mean_img"] = self._gen_fname(outputs["out_file"] + "_mean_reg.ext", cwd=output_dir)
            else:
                outputs["mean_img"] = self._gen_fname(
                       outputs["out_file"],
                       suffix="_mean_reg",
                       cwd=output_dir)

⁠4. Command for creating container

docker run -it --gpus all -m 16g \
-p 6000:22 -p 7777:5925 \
-v /path/to/freesurfer_license.txt:/opt/freesurfer/license.txt \
-v /other/dir/you want to map/:/root/uestc \
--name dwitool uxhao/dwitool:mrtrix3.0.8_fsl6.0.7.19_freesurfer7.4.1_ants2.6.3_mr3tissue5.2.9