Download demo data for recon practice from OSF course page

Access FastX through the remote login:
https://fastx.divms.uiowa.edu:3443/

First prep step, make a folder for holding data for our class:

• Open your terminal by clicking on the icon showing a little black screen
• Type pwd. Where are you in the computer filesystem?
• Type ls. What other files are here?
• To make a new folder using the terminal type mkdir fmrilab

Second prep step, download demo images:

• Copy/paste wget -O ReconDemo.tar.gz https://osf.io/2n9wk/download
• Use commands introduced above to see what was downloaded
• To unpack the download copy/paste tar -xvf ReconDemo.tar.gz
• Move yourself into the folder with data by typing cd ReconDemo
• Let's compare what is in the folders we've downloaded using the GUI file browser and the terminal

Now we are ready to practice with dcm2niix!

Refer to usage notes here

Base usage example:

dcm2niix /path/to/dicom/folder

Exercise 1: What would this look like for our data? dcm2niix DICOM/files

Exercise 2: How can we modify the command line arguments so that the reconstructed data goes to our anat_T1w folder? dcm2niix -o ~/fmrilab/ReconDemo/anat_T1w DICOM/files

Exercise 3: How can we modify the call so that we get a "bids sidecar" .json file? This will be a .json file that specifies meta data with the BIDS naming conventions for MRI data. dcm2niix -b y -o ~/fmrilab/ReconDemo/anat_T1w DICOM/files

Exercise 4: How can we name our filename is output as protocol_participantID dcm2niix -z y -b y -f %p_%i -o ~/fmrilab/ReconDemo/anat_T1w DICOM/files

Exercise 5: View the nifti image with fsleyes. Use the terminal to change directories to where the image is and type fsleyes VOSS_CLASS_20231017.nii.gz. You should see a T1 weighted anatomical image!