10. STEP 3.1 (after DIFFPREP):DR-BUDDI


DR-BUDDI performs EPI distortion correction using two datasets with opposite phase encoding directions. If you have acquired data with opposite phase encoding direction, please skip the EPI correction in DIFFPREP and do the DRBUDDI correction as described below.It is adviced that DRBUDDI be first run with the default settings. The only inputs required are blip up data proc.list, blip down data proc.list, an anatomical image-preferrably T2W fat suppressed image. Other advanced settings listed in the help file are incorporated in the run and used internally. If the results do not look satisfactory, you may change few of the advanced settings to fine tune. If you need further assistance with the settings please contact the TORTOISE support team.

The latest version of TORTOISE ver3.2 has capability to run DRBUDDI without a structural data. If the structural data is subpar, DRBUDDI 3.2 can be run without it and utilize the information from the blip and down DWI data. Under 3.2, if the tag --do_not_use_structural 1  is used, then the structural provided will only be used as a reorientation template for the final output corrected data. 

An example scenario: If you have a test dataset with Subject1_DTI_UP (blip up) and Subject1_DTI_down (blip down), both will have to go through DIFFPREP processing separately to generate Subject1_DTI_up_proc.list and Subject1_DTI_down_proc.list that are generated within each of the up and down proc folders. These are the inputs to DR-BUDDI together with the structural image (for best results, it is best to use a T2 W fat suppressed dataset).

Note: Two additional parameters have been introduced in DRBUDDI3.1.3 and above versions, which were not present in the 3.0 version. They are the gradient non linearity correction. If you intend to use these correction measures, you will have to use 3.1.3 or above versions for all import and DIFFPREP processing as well. Please refer to change log for latest changes to TORTOISE. 

The screenshot below shows the DRBUDDI help file that is displayed in the terminal upon typing the command: DR_BUDDI_withoutGUI for version 3.1.3.  

Change log documents the upgrades and if additional changes are beneficial, please incorporate the latest TORTOISE version in your processing.  

Screenshot of DRBUDDI help file for version 3.1.3

The expected folder after running DRBUDDI could be a folder ending in *_proc_DRBUDDI_proc, as seen in the screenshot below:

DRBUDDI processing main folder

***Please note: You may create an output folder using mkdir and provide the full path to the new output folder generated with the output list file name of choice in the DRBUDDI command line using the -o tag.  The results of DRBUDDI will be created in the new output folder using the list file provided in the -o tag.***

Folders Description
DTI_down folder containing the raw down data pre-import
DTI_up folder containing the raw up data pre-import
subject1_DTI_up_proc folder generated post import, renamed to add a prefix ‘subject1_DTI’. It contains all the files decribed in the DIFFPREP outputs sections. In addition, after running DRBUDDI, there will be files ending in _’DRBUDDI’. These are the ‘DRBUDDI corrected UP’ files. This is not the final DRBUDDI output but only the output before combining with the down data.
subject1_DTI_down.proc The same decription as for the subject1_DTI_up_proc, except the file names here will be subject1_DTI_down.
subject1_DTI_up_proc_DRBUDDI_proc This is the final DRBUDDI folder that contains all the files that will be decribed in the ‘outputs of DRUDDI’ section.
T2_acpc.nii The subject specific T2 file that will be used in the DRBUDDI processing. Please note, this file can exist anywhere but has been included here, in the main folder, to be organised.

10.1. DRBUDDI outputs

DRBUDDI outputs


Outputs of DIFFPREP processing Description
command.log test file that describes the command used in DRBUDDI processing
blip_up_b0.nii Uncorrected b0 from ‘up’ data
blip_down_b0.nii Uncorrected b0 from ‘down’ data
blip_up_dwi_* synthesized DWIs generated from the ‘up’ data. Default will be four nii files will be generated from dwi_0 to dwi_4 as the disortion level set is ‘medium’. For disortion setting ‘large’,six nii files will be generated from dwi_0 to dwi_5 will be generated.
blip_down_dwi_* synthesized DWIs generated from the ‘down’ data. Default will be four nii files will be generated from dwi_0 to dwi_4 as the disortion level set is ‘medium’. For disortion setting ‘large’,six nii files will be generated from dwi_0 to dwi_5 will be generated.
blip_up_quad uncorrected ‘up’ b0 that now is at the resolution of the structural_used.nii
blip_down_quad uncorrected ‘down’, b0 that now is rigidly registered to the structural_used.nii
blip_up_b0_quad.hdf5 transformation binary text file
blip_up_b0_quad.hdf5 transformation binary text file
deformation_FINV.nii.gz and deformation_MINV.niig.gz deformation fields generated after b0’s are registered to structrual
structural.nii original structural file input when running DRBUDDI. The final DRBUDDI outputs will be in the space of the input structural file.
structural_used.nii The structural.nii is now in the space of the ‘up’ b0.nii. Please see the note below for additional details
blip_up_b0_corrected.nii ‘up’ b0 now is corrected for distortions using information from the structural_used.nii
blip_down_b0_corrected.nii ‘down’ b0 now is corrected for distortions using information from the structural_used.nii
b0_corrected_final.nii the geometric mean of the ‘blip_up_b0_corrected.nii’ and ‘blip_down_b0_corrected.nii’.
subject1_DTI_up_proc_DRBUDDI_final.bmtxt the final bmtxt of the corrected data in the space of the structural.nii i.e the space of the strutural file that you gave as input when running DRBUDDI.
subject1_DTI_up_proc_DRBUDDI_final.list the final list file that points to the final bmtxt and final nii file. You will need to use
subject1_DTI_up_proc_DRBUDDI_final.nii the final combined up and down diffusion data in nii format


Note: In TORTOISE 3.1 and above versions, the final DRBUDDI outputs in DRBUDDI_proc folder will be in the final space of the structural provided during processing i.e _finalDRBUDDI will be in the space of structural.nii. The intermediate files such as up and down quad, up and down corrected and final b0 will all be in the space of structural_used.nii. The structural_used.nii in fact is in the space of the up_b0.nii space. So, when you visualize these intermediate files, you may find that they may not be in the standard orientation that you would expect the final images to be in. Only the final images will in the final orientation of the structural provided during processing.

10.2. If UP and DOWN bmtxts or number of volumes do not match

If your data has up and down bmtxts that do not match i.e with unequal number of volumes between the pair, DRBUDDI3.1 and above versions will run but will output an warning message in the terminal indicating that the up and down data will not be combined. If the number of volumes and bmtxts do not match, DRBUDDI will now automatically output the geometrically corrected and signal manipulated versions of both up and down data. You have the option to combine the two separate *DRBUDDI.list files generated within the DRBUDDI folder, using the CombineListFiles present in the DIFFPREP/bin/bin directory. The combinelist files command will  generate a concatenated .list file, with output name of choice, to fit the tensor. Please go through the volumes, opening the resulting .nii file after combining to ensure that the combined file looks okay to be used in tensor fitting. If the quality is subpar and you notice differences in correction between the pair, combining them is not advisable. 

If not combining, then one can fit the tensor only to the *DRBUDDI.list  corresponding to the data with higher number of DWIs of the pair. 

Note: Please cite the following, if you DRBUDDI: DR-BUDDI (Diffeomorphic Registration for Blip-Up blip-Down Diffusion Imaging) method for correcting echo planar imaging distortions,M Okan Irfanoglu,Pooja Modi, Amritha Nayak,Elizabeth B Hutchinson, Joelle Sarlls, Carlo Pierpaoli,NeuroImage,2015,February 1,106:284-99