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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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Hi!
Apart from the entertaining discussion about the name of these atlases, I was wondering whether the hemisphere-specific ROIs will be made available any time soon (last update on that here on the message board was in January). If not, would you mind posting instructions on how to split the existing ROIs in CHARM?
Thank you very much!
by
casparms
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AFNI Message Board
Hi!
I was wondering whether there is any update on this?
If not, would it be possible to post info on other solutions to hemisphere-specific labels?
Thanks!
by
casparms
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AFNI Message Board
Hi!
Is there already an update on the bilateral ROIs?
Thank you,
Caspar
by
casparms
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AFNI Message Board
Hi!
I am wondering how to access the CHARM atlas ROIs per hemisphere.
Is there an example available somewhere or could be posted here?
Thank you!
Caspar
by
casparms
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AFNI Message Board
Hi!
I used 3dUniformize -anat VMR.ss+tlrc -prefix VMR.ss_norm for the normalization.
Regarding the alignment, I got it to work now by first running Align_centers and then using the shifted data set as input to align_epi_anat.py; the other important change was to use -EPI in the Allineate_opts.
Caspar
by
casparms
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AFNI Message Board
Hi Rick,
thanks for the advice!
This is the output of afni -ver
Version AFNI_2011_12_21_1014
[]
Following your input, I played around with the filenames a bit, and I don't get the error anymore:
anatomy=VMR.ss+orig
tlrc_anatomy=VMR.ss+tlrc
epi=EPI+tshift+moco+wrap+orig
align_epi_anat.py -epi $base_folder/$data_folder/EPI+tshift+moco+wrap+mask+orig -anat $base_folder/$an
by
casparms
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AFNI Message Board
Hi!
I am trying to align 7T EPI data from rats to T1s and to the new Waxholm rat template.
When using align_epi_anat.py, I get the following error message, which leaves me clueless:
NameError: global name 'anat_tlrc' is not defined
This is my command line:
anatomy=VMR.ss+orig
tlrc_anatomy=VMR.ss_norm+tlrc
epi=EPI+tshift+moco+wrap+orig.BRIK
align_epi_anat.py -epi $base_f
by
casparms
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AFNI Message Board
I'd be interested in these scripts and guidelines, if available.
I think I fulfill the criteria ;)
Thanks, Caspar
by
casparms
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AFNI Message Board