re: rodent data

Submitted by nmskhan on


I was trying to run the rodent data on the tortoise, i was not sure about what is big bang in the diffprep module. What are the correct default settings for rodent data, all I have is, a 2 b-values, 14 directions, spin-echo based DTI data? Anything I have to uncheck before running this?

what is big delta and small delta in the import module? is this time between two diffusion gradients and separation? or something else?

In the DRBUDDI mode, what are files to be input to this page? What are path to up or path to down files? Confused? I do not have a path up or down files? Could you please shed some light on these?

The explanation on the website is not clear.




Submitted by nayaka on Fri, 07/19/2019 - 18:17


Hi Ned,

Which version of TORTOISE are you using?

The big bang in DIFFPREP is the start of processing, essentially step 0. You do not need to prescribe it as without it the assumption is that it will run through all the steps to give you the final result. 

For rodent data, as an initial go, please run DIFFPREP using default settings but uncheck the 'is_human_brain' to be 0. This will call a separate settings files,internally, that is more geared towards working on non human data. You may also provide the desired output resolution. If the data correction look good, you can go ahead with the default settings. 

DIFFPREP in addition to performing eddy and motion distortion correction, it also performs EPI distortion correction and is limited to image based registration relying on the structural data provided.

DRBUDDI module is only used if you have data that has been acquired with reverse phase encoding, i.e blip_up and blip_down data, mainly with the intention of performing more advanced EPI distortion correction. To use this module one of the requirement is that you have to have run the eddy motion correction through DIFFPREP, until step3, separately on blip up and blip down data resulting in output files detailed under the DIFFPREP software guide. Since generally the _proc.list required as inputs to DRBUDDI are each inside blip up_proc and blip_down_proc folders, the user will have to provide the path to these _proc.list file to DRBUDDI module in the following syntax:

DRBUDDI   --up_data  <path_to_up_proc.list>  --down_data  <path_to_down_proc.list>   <optional arguments>

If you do not have up and down data, then your processing pipeline will end at DIFFPREP (run completely till the last step) resulting in _DMC.list, DMC.nii and DMC.bmtxt files. The tensor will then be performed on the _DMC.list file. 

If you have blip up blip down data, then the processing pipeline will be as follows: perform DIFFPREP separately for blip_up and blip_down data. You can shorten the process by checking the tag 'will_be_drbuddied' (tag only applicable to versions v3.0 and above). This will only run it until step 3 and there will _proc.list files in each of the blip_up_proc and blip_down_proc. You will then use the blip_up_proc.list and blip_down_proc.list in the DRBUDDI processing to perform the extended EPI correction, where information from up and down data will be combined to give you the final EPI corrected DRBUDDI_final.nii, DRBUDDI_final.list and DRBUDDI_final.bmtxt files.  The tensor fitting in this case will be performed on the DRBUDDU_final.list file.