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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:
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
| October 10, 2017 10:25AM | |
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).
My first question is can I use whereami to obtain a label from a standard atlas (like Talairach daemon) if my dataset is in ORIG space?
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?
On a side note, I am considering getting all of my datasets in TT space using @auto_tlrc as a preprocessing step, then feeding these datasets into freesurfer so that I can use both the TT daemon and the freesurfer segmentations/parcellations with whereami.
Thanks,
Mike
Edited 1 time(s). Last edit at 10/10/2017 10:32AM by mstrotta.
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).
My first question is can I use whereami to obtain a label from a standard atlas (like Talairach daemon) if my dataset is in ORIG space?
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?
On a side note, I am considering getting all of my datasets in TT space using @auto_tlrc as a preprocessing step, then feeding these datasets into freesurfer so that I can use both the TT daemon and the freesurfer segmentations/parcellations with whereami.
Thanks,
Mike
Edited 1 time(s). Last edit at 10/10/2017 10:32AM by mstrotta.
| Subject | Author | Posted |
|---|---|---|
|
mstrotta | October 10, 2017 10:25AM |
|
mstrotta | October 15, 2017 08:24PM |
