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

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jwest
March 21, 2023 10:20AM
hello afni users



I have an image that is correctly aligned in native space but when the image is warped to standard space the image becomes skewed and unusable. However, it is only affecting certain subjects. I do not understand why some subjects are not affected and others are. I am using the uber_subject.py gui to create the preprocessing scripts.

here is the script line where the images seemed to be not correctly aligned.

@auto_tlrc -base MNI_avg152T1+tlrc -input warped_ns+orig -no_ss -init_xform AUTO_CENTER

is there a way to correct the alignment at the tlrc level.

i have attached a screen shot of the skewed image.

thank you for any help with this

jef
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Attachments:
open | download - screeenshot_skewed.png (561.9 KB)
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Subject Author Posted

incorrect tlrc correction Attachments

jwest March 21, 2023 10:20AM

Re: incorrect tlrc correction

ptaylor March 21, 2023 02:16PM

Re: incorrect tlrc correction

jwest March 22, 2023 01:09PM

Re: incorrect tlrc correction

ptaylor March 23, 2023 09:25AM