DIFFPREP

Dear experts,

I ran DIFFPREP command to perform distortion correction using structural data. I used --step 0, assuming that all three corrections would be performed. But in the final image I expected to see an output file  with generic name _EPI_field.nii. I got an output(the name that I specified in -o flag) .nii. Does this mean that epi distortion has been done?

I'm using Tortoise 3.2.0 GUI, when I run DIFFPREP I get

"Invalid entry in the listfile Not all the mendatory tags present in the listfile...Exiting..."

What does this mean and how do I fix it?

Thanks

Hi!
Do I understand correctly, that if I want to use TORTOISE for eddy correction before processing in 3D Slicer I need _DMC.nii output and my .bval and .bvec?

Trying to run Diffprep on a test subject with multi-shell DWI and I ended up with a segmentation fault after many hours of EPI correction. Script is running on research computing machine with 12 cores and 8gb of ram per core, so memory shouldnt be an issue. Any ideas? Here is my code:

As FLAIR image is similar to T2w image,  does it can be used as structural image in DIFFPREP?

Can TORTOISE use field mapping to correct distortions?

Thanks!

Update on 9/8/20:

It turned out that the registration setting was not correctly loaded though the path of the dmc file was assigned in GUI and placed in diff_prep_work folder. Once the parameters were manually entered in the advanced registration options, the registration processing did not return any warning messages.

_________

Hello,

Hi Tortoise!

Hello,

I have a few questions about the mec files for DIFF PREP.

I am using DIFF PREP on ex-vivo specimens that are not expected to move during the scan.
Is it possible to create a mec file that corrects only for eddy currents but not motion?

In the mec file, there are optimization and bracketing epsilons.
How are these epsilons used during the optimization process?

Hi,

I would like to use TORTOISE on a data set for which T1, and not T2, structural data were collected. I read about a work-around for using T1 images here which seems to involve attenuating non-brain regions. Apparently this suggestion came from a TORTOISE developer. I just want to make sure that this would be valid and/or necessary to do in the most recent version of TORTOISE (3.2.0 at time of writing). 

Thanks,

Steven