AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

|
August 15, 2019 09:50AM
Hello,

I am running am trying to run my dwi data through TRACULA and for two of my subjects I was unable to run the command orientLAS.
After using 3dinfo on the data set I found that the two subjects that didn't run had a Data Axes Tilt: Oblique (45.000 deg. from plumb)


My data set

Data Axes Tilt: Oblique (43.300 deg. from plumb)
Data Axes Tilt: Oblique (38.100 deg. from plumb)
Data Axes Tilt: Oblique (42.100 deg. from plumb)
Data Axes Tilt: Oblique (32.400 deg. from plumb)
Data Axes Tilt: Oblique (41.700 deg. from plumb)
Data Axes Tilt: Oblique (42.300 deg. from plumb)
Data Axes Tilt: Oblique (45.000 deg. from plumb) (didn't work)
Data Axes Tilt: Oblique (37.900 deg. from plumb)
Data Axes Tilt: Oblique (34.300 deg. from plumb)
Data Axes Tilt: Oblique (31.700 deg. from plumb)
Data Axes Tilt: Oblique (31.800 deg. from plumb)
Data Axes Tilt: Oblique (27.500 deg. from plumb)
Data Axes Tilt: Oblique (38.900 deg. from plumb)
Data Axes Tilt: Oblique (45.000 deg. from plumb) (didn't work)
Data Axes Tilt: Plumb
Data Axes Tilt: Oblique (13.200 deg. from plumb)

When I applied 3wdarp -deoblique to the dwi images and then ran them through TRACULA and orientLAS for fsl it worked, however, now I am worried if this will cause an issue with eddy current correction. Do I need to modify the bvecs and bvals for the subjects where I use -deoblique on them before eddy current correction? Sorry, I am not super comfortable with how afni treats obliquity.
Subject Author Posted

3dwarp -deoblique and dwi data need to correct bvals and bvecs?

2Daniel4 August 15, 2019 09:50AM

Re: 3dwarp -deoblique and dwi data need to correct bvals and bvecs?

ptaylor August 15, 2019 11:28AM

Re: 3dwarp -deoblique and dwi data need to correct bvals and bvecs?

2Daniel4 August 16, 2019 06:56AM

Re: 3dwarp -deoblique and dwi data need to correct bvals and bvecs?

Tahereh July 26, 2021 03:37AM

Re: 3dwarp -deoblique and dwi data need to correct bvals and bvecs?

Tahereh August 01, 2021 03:29AM