DIFFPREP

Dear all experts,

I used the DIFFPREP to preprocess my data, and there is a output *_DMC_noise.nii file. But I have no idea what it means. Is it the standard deviation of rician noise? If not, could the standard deviation of rician noise be gotten in TORTOISE?

Looking forward your reply. Thanks very much.

Zhaoqing

Hello,

I am trying to run DIFF_PREP, but it's taking up a lot of resources and making my machine really hot when running it. I tried putting an NCPUs.cfg file in DIFF_PREP_WORK to limit it to one core, but that doesn't seem to help. Is there another way to limit the resources used by DIFF_PREP (and other TORTOISE programs)? I am running on Mac Mojave i7. My diff prep call is below:

DIFFPREP -i /Users/tortoise_testing/tortoise_testing.list --do_QC 1 --will_be_drbuddied 1 --reg_settings example_registration_settings.dmc 

Thanks, 

Amy

Hi, 
 

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?