I might need some support to convert my data to the BIDS format. Specifically, I am currently having a hard time understanding the type of data to be included in the “anat” subfolder. Specifically, what does “inplane” t1 and t2 refer to? In my data, I have my mprage, and EPI task. In other words, is it ok to only input my de-identified mprage in “anat” and epi task (+events) in “func”?
Also, I am currently trying to use mri-deface, but when I try to execute the following inline “./mri_deface sample_T1_input.mgz talairach_mixed_with_skull.gca face.gca sample_T1_input_defaced.mgz” Terminal says: “-bash: ./mri_deface: Permission denied”
A GUI wrapper for dcm2niix is provided with MRIcroGL - choose the “Convert DICOM to NIfTI” menu item from the “Import” menu. The GUI not only converts your data, but it shows you the resulting terminal command as well. Therefore, you can get used to the graphical interface and then easily copy and paste your desired conversion into a script. If you prefer Matlab, the dicm2nii provides a nice graphical interface.