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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

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eji
December 05, 2020 03:09AM
Hello, I realized that some of our diffusion data are oblique, therefore I used 3dWarp to deoblique. I then checked the output using 3dinfo. While the angle from plumb is now 0, it appears that the matrix size has changed. It would be helpful if someone could explain why this happened and confirm whether this should be fixed. Thanks!

Below I pasted the input commands of 3dWarp and 3dInfo and also the output of 3dInfo.

cd SPN01_ZHP_0060_01/afni;
3dWarp \
-deoblique \
-prefix dwi_ec_deob.nii.gz ../data.nii.gz \
-overwrite


3dinfo \
-is_oblique \
-obliquity \
-same_grid \
-n4 \
-ad3 \
-prefix \
$dtipath/SPN01_ZHP_0060_01/data.nii.gz \
$dtipath/SPN01_ZHP_0060_01/afni/dwi_ec_deob.nii.gz

1 5.837 0 128 128 66 60 2.000000 2.000000 2.000000 data.nii.gz
0 0.000 0 134 138 82 60 2.000000 2.000000 2.000000 dwi_ec_deob.nii.gz

(also, what is the column of 60s? It doesn't seem to belong to n4 or ad3)



Edited 1 time(s). Last edit at 12/05/2020 03:11AM by eji.
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Subject Author Posted

3dWarp changes matrix size?

eji December 05, 2020 03:09AM

Re: 3dWarp changes matrix size?

ptaylor December 05, 2020 11:11AM

Re: 3dWarp changes matrix size?

eji December 07, 2020 10:28AM

Re: 3dWarp changes matrix size?

ptaylor December 07, 2020 04:19PM

Re: 3dWarp changes matrix size?

eji December 08, 2020 02:19AM