Using .nii file as my DWI Nifti file, keeps saying does not exist, I have tried putting full path to file all the way from root and still not being found.
It seems fro the command you are using you are attempting an import?
For TORTOISE processing you first need to import the data into tortoise format i.e list, bmtxt and nii file housed inside the _proc folder. This can be done as follows:
For your diffusion data you can follow these steps:
1) It is adviced that you create two folders containing ...008a1001.nii and ...009a1001.nii, seprately. These folders should also contain their associated bval and bvec file. This is because if there are more than one bval or bvec file in a folder (the way it is in the screenshot you have attached) the import complains and will not proceed.
2) after separation, please import the nii file from their folders, created in step1, by using the following syntax: ImportNIFTI -i <full_path_to_nii_to_import> -p vertical
This should create _proc folder for each other diffusion data you are importing.
3) Within the _proc folder there will be .list, .bmtxt and .nii file. You can now use the .list file to run the DIFFPREP processing using the following syntax:
DIFFPREP -i <full_path_to_list_file> -s <t2_structrual_reference> --any other optional arguments
hope this helps.