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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:
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
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
| May 31, 2017 09:11PM | |
Hey,
Is 3dAutomask (generally) more generous in it's estimation of the brain when skullstripping EPI images than 3dSkullStrip?
I ask because in this screen shot
(run on the same data from the same subject), on the left can be seen an invocation of align_epi_anat.py with 3dSkullStrip as the default and on the right is an invocation of aea with 3dAutomask as the skull stripper. Both invocations produce good alignments but the extent of the brain from the invocation involving 3dAutomask is clearly bigger.
Is there a reason to prefer 3dAutomask over 3dSkullStrip fro skullstripping EPI data?
LEFT AFNI:
RIGHT AFNI:
Is 3dAutomask (generally) more generous in it's estimation of the brain when skullstripping EPI images than 3dSkullStrip?
I ask because in this screen shot
(run on the same data from the same subject), on the left can be seen an invocation of align_epi_anat.py with 3dSkullStrip as the default and on the right is an invocation of aea with 3dAutomask as the skull stripper. Both invocations produce good alignments but the extent of the brain from the invocation involving 3dAutomask is clearly bigger.
Is there a reason to prefer 3dAutomask over 3dSkullStrip fro skullstripping EPI data?
LEFT AFNI:
align_epi_anat.py -anat2epi \
-anat ${anatFile} \
-epi ${epiFile} \
-epi_base 0 \
-volreg off \
-tshift off \
-cost lpc \
-multi_cost lpa lpc+ZZ mi
RIGHT AFNI:
align_epi_anat.py -anat2epi -anat bc002b.anat_unif+orig \
-suffix _al_keep \
-epi vr_base+orig -epi_base 0 \
-epi_strip 3dAutomask \
-cost lpc \
-volreg off -tshift off
| Subject | Author | Posted |
|---|---|---|
|
Colm Connolly | May 31, 2017 09:11PM |
|
rick reynolds | June 08, 2017 08:31PM |
|
Daniel Glen | June 09, 2017 04:06PM |
