DIFFPREP

We are currently running DIFFPREP on some data we have collected. We are running the DIFFPREP function (TORTOISE V3.2.0) on Linux  on Ubuntu 20.04.  Below is our currently input:

DIFFPREP --dwi ~/Desktop/Tortoise_DTI/Tortoise/1007/diffusion_data.nii --bvecs ~/Desktop/Tortoise_DTI/Tortoise/1007/bvecs  --bvals ~/Desktop/Tortoise_DTI/Tortoise/1007/bvals -p vertical -s ~/Desktop/Tortoise_DTI/Tortoise/1007/T2_acpc.nii --unsampling all --keep_intermediate 0

Hello,

Hi TORTOISE experts. Thanks for your nice and handy software.

My question is about rotating bvec. Basically, I have data which has been acquired 90 degrees rotated from stereotaxic orientation, on a Siemens Magnetom Prisma 3T scanner. Both anatomical (T1,T2) and DWI (AP-PA) data have this 90 degree rotation. So when I rotate them back to normal (stereotaxic) orientation in AFNI, I think I should compensate for this rotation by re-adjusting the bvec file, right? So, is this something I can do in TORTOISE or should I try to do it in AFNI?

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.

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Hello,