Submission demo

[agahkarakuzu]

Name: Agah Karakuzu

Number of datasets (sets of inversion recovery measurements: 1

Submission Checklist:

• [x] Have you collected all the raw data exported directly from scanner into a single folder?
• [x] For each dataset, did you create one (or two, if complex) NIFTI files with each inversion time measurement in the "time" dimension?
• [x] For each NIFTI file, did you create a YAML file with the same filename containing the necessary details about your dataset for the challenge? (See sample submission on OSF.io for a template)

[agahkarakuzu]

Hi Mathieu,

I was able to easily create this using dcm2niix and fslmerge.

1. I put all my *.dcm images in one folder and called dcm2niix on them one by one to create NIFTI images:

Before:

├── ds-NIST
└── IR-T1
         ├── TI_50.dcm
         ├── TI_400.dcm
         ├── TI_1100.dcm                     
         └── TI_2400.dcm   

After:

├── ds-NIST
└── IR-T1
         ├── TI_50.nii
         ├── TI_50.json
         ├── TI_400.nii
         ├── TI_400.json
         ├── TI_1100.nii
         ├── TI_1100.json
         ├── TI_2400.nii                                  
         └── TI_2400.json   

2. I used fslmerge with the following call to merge them:

fslmerge -t 20201002_karakuzu_neuropoly_NIST.nii.gz TI_50.nii TI_400.nii TI_1100.nii TI_2400.nii

This created the 4D 20201002_karakuzu_neuropoly_NIST.nii.gz. You can see that it has 4 components:

3. I used the *.yaml template you shared in OSF and filled that out with my information to create:

20201002_karakuzu_neuropoly_NIST.nii.gz

In the next comment, I'll explain how to do fslmerge using Docker.

[agahkarakuzu]

After dcm --> nii conversion, you can do fslmerge in a Docker container if you don't have FSL installed to your computer.

Assuming that you can use Docker:

1. Open your terminal.
2. docker pull qmrlab/anstfsl
3. export my_nii_folder=/Users/Agah/Desktop/ds-NIST/IR-T1 Change this to point to your directory with *.nii images.
4. docker run -it --rm -v $my_nii_folder:/tmp qmrlab/antsfsl. This command will start an interactive container session. From the next step on, the commands will be executed on qmrlab/antsfsl container.
5. cd /tmp
6. Make sure that ls command should list

   ├── TI_50.nii
        ├── TI_50.json
        ├── TI_400.nii
        ├── TI_400.json
        ├── TI_1100.nii
        ├── TI_1100.json
        ├── TI_2400.nii                                  
        └── TI_2400.json   

7. fslmerge -t 20201002_karakuzu_neuropoly_NIST.nii.gz TI_50.nii TI_400.nii TI_1100.nii TI_2400.nii
8. exit

The merged *.nii will be available at the directory (/Users/Agah/Desktop/ds-NIST/IR-T1) I mounted to the Docker container.

[agahkarakuzu]

I went ahead and fit the data using qMRLab: