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DIFFPREP

Limit CPU usage of DIFF_PREP

Submitted by amirro on Tue, 01/11/2022 - 10:49
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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

SyN Registration Error

Submitted by nkraus on Mon, 10/11/2021 - 13:49
Category

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

 

bvec rotation

Submitted by Tahereh on Tue, 07/27/2021 - 02:52
Category

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?

DIFFPREP- EPI DISTORTION CORRECTION

Submitted by Ashika on Fri, 05/07/2021 - 04:26
Category

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?