SyN Registration Error

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

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

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?


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

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?


Warning message during registration process (solved 9/8/20)

Submitted by rku on Wed, 09/02/2020 - 16:26

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.