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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boukes01
August 08, 2022 02:08PM
Hi AFNI world,

I want to normalize a partial volume to the MNI using the code below:

@auto_tlrc -base MNI_caez_N27+tlrc -input 5004_UNI+orig
align_epi_anat.py -anat 5004_UNI+orig -epi 5004_npu1_nat+orig \
-epi_base 6 -child_epi 5004_npu2_nat+orig.HEAD 5004_npu3_nat+orig.HEAD \
-partial_axial \
-ex_mode quiet -epi2anat -suffix _altest \
-tlrc_apar 5004_UNI+tlrc

5004_UNI+orig corresponds my structural image, 5004_npu1_nat+orig corresponds to the first run of my fMRI task, 5004_npu2_nat+orig.HEAD and 5004_npu3_nat+orig.HEAD correspond to run2 and run3 of the task in their native space.

The script is running smoothly, however, when I observe the output image (see screenshot attached) I don't understand why I observe these yellow signals a little bit outside of the brain. Am I doing something wrong?

Any help would be appreciated.

Thanks,

Sarah.
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partial axial normalization Attachments

boukes01 August 08, 2022 02:08PM

Re: partial axial normalization

ptaylor August 08, 2022 07:55PM