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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brainboi
March 11, 2023 11:19AM
Hi Rick,

Thanks for the response! I tried 3dSkullStrip instead but the results look the same. In this case though, I do get this in the terminal output: 
#++ removing skull or area outside brain
#Script is running (command trimmed):
  3dSkullStrip -orig_vol -input ./__tt_vr_base_min_outlier_unif_ts_rs+orig -prefix ./vr_base_min_outlier_unif_ts_rs_ns
oo     Warning 3dSkullStrip (SUMA_3dSkullStrip.c:1649):
Input dataset has a very low value range.
If stripping fails, repeat with option -fac 1000

At this suggestion, I added -skullstrip_opts -fac 1000 to my afni_proc.py command so the proc script looks like this: 
align_epi_anat.py -anat2epi -anat anatSS.AB1056+orig        \
       -suffix _al_junk                                     \
       -epi vr_base_min_outlier_unif+orig -epi_base 0       \
       -epi_strip 3dSkullStrip                              \
       -anat_has_skull no                                   \
       -cost lpc+ZZ -check_flip -skullstrip_opts -fac 1000 \
       -volreg off -tshift off

However, I am still getting the same result and terminal output as before, so I'm unsure if 3dSkullstrip is applying the -fac 1000 option. Do you happen to have any other suggestions?

Sincerely,
Ian
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Subject Author Posted

Anat-EPI Alignment Troubleshooting Attachments

brainboi March 10, 2023 02:36PM

Re: Anat-EPI Alignment Troubleshooting

rick reynolds March 10, 2023 03:54PM

Re: Anat-EPI Alignment Troubleshooting

brainboi March 11, 2023 11:19AM

Re: Anat-EPI Alignment Troubleshooting

ptaylor March 12, 2023 08:57AM

Re: Anat-EPI Alignment Troubleshooting Attachments

brainboi March 20, 2023 06:05PM

Re: Anat-EPI Alignment Troubleshooting

ptaylor March 20, 2023 08:10PM

Re: Anat-EPI Alignment Troubleshooting

ptaylor March 21, 2023 09:23AM

Re: Anat-EPI Alignment Troubleshooting

brainboi March 23, 2023 06:48PM