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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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Bumping this topic. I am likewise looking for a way to convert the Desikan-Killiany ("aparc") atlas to standard-node space. Any resolution to this? It would be nice if this were a default step of SUMA_Make_Spec_FS.
by
mstrotta
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AFNI Message Board
Hi,
I can't get align_epi_anat.py to run without using an autoweight in 3dAllineate. From the documentation, I would think passing 3dAllineate_opts "-nomask" should do the trick, but it doesn't:
#++ Aligning dset1 data to dset2 data
#Script is running (command trimmed):
3dAllineate -mi -wtprefix ./__tt_mr_pre_ob_al_wtal -weight ./__tt_ct_implant_res_shft_ts_wt+orig -
by
mstrotta
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AFNI Message Board
> My second question is: suppose I have run
> Freesurfer and @SUMA_make_spec_FS and thus have
> aseg.nii and aparc*+aseg*.nii datasets. Since I
> gave Freesurfer surfaces in ORIG space, I should
> be able to lookup the label for any xyz coordinate
> in the subject's native space. Can I use
> whereami to obtain a label from a subject-specific
> FS atlas?
>
by
mstrotta
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AFNI Message Board
I can address one of your questions--the error:
** ERROR: Unknown space_name ORIG
whereami NULL string out.
Looks like this error comes from there not being any ORIG template space. I've been able to resolve this error by adding the following xml block to the subject's SessionAtlases.niml file (note you could also add this to a more general location where afni looks for atlases,
by
mstrotta
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AFNI Message Board
Hello!
I am wondering if afni's whereami command can be run on a dataset that is still in its ORIG space and hasn't been aligned with a Talairach, MNI, or other template. It seems to be disabled on the GUI for ORIG space datasets (although you can still run the command line utility for the dataset, perhaps the returned atlas information isn't necessary meaningful or correct).
by
mstrotta
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AFNI Message Board