I have previously created ROI:s using e.g.
Make ACC mask named ACC_mask
whereami -prefix ACC_mask -mask_atlas_region ‘TT_Daemon::ACC’
Make Insula mask named insula_mask
whereami -prefix insula_mask -mask_atlas_region ‘TT_Daemon::insula’
I think the whereami command is kind of complicated and I get stuck now that we have swapped to the MNI152_2009_template.nii.gz as our template during pre-proc.
I saw a lot of old posts asking similar questions but in 2013 AFNI did not offer atlases for MNI space and the MNI_ANAT was apparently shifted in regard to the MNI space.
I simply wan to create a hypothalamus ROI using something like
whereami -prefix hyp_thal_ROI -mask_atlas_region ‘MNI??::hypothalamus’
but I don’t know the name of a potential MNI-atlas and what that sub-region would be called.
Can someone help?
An easy way to get a listing of all ROIs across all of the atlases that you have loaded is:
Hypothalamus isn’t that common in the atlases that I usually look through, but you could take the TT version and transform it using either 3dWarp’s -tta2mni option or by creating a transform (preferably with either auto_warp.py or 3dQwarp) and apply that tranform to move your region of interest from one space to another.
Peter is right; the hypothalamus is curiously missing from almost all commonly available atlases except for the Talairach daemon. We have the Keuken sub-cortical atlas available, but it is also missing the hypothalamus. I did a little research to find some others and found some good leads. You can look yourself at these, but this recent one was easy to get working with AFNI and integrated with whereami.
Download and expand tgz file
tar xzvf subcortical_dist.tgz
@AfniEnv -set AFNI_SUPP_ATLAS_DIR
The hypothalamus is labeled “HTH” in the linked atlas.
I am the same problem.
Can you explain better the whereami function?
When I ask: whereami -show_available_spaces TLRC, the answer is:
++ ----- List of available spaces: -------
However, if I try:
whereami -mask_atlas_region TT_Daemon:right:putamen -prefix Putamen_right -space MNI
There is an error:
++ Input coordinates orientation set by default rules to RAI
Best match for putamen:
Right Putamen (code 151)
** ERROR: Atlas does not match space requested.
What is wrong?
That function produces a dataset for that region. It does not transform the region to the space of the dataset. See the other posts on this messageboard for the various ways of how to do that.
I just did this for the amygdala in MNI space so this’ll probably work for you.
whereami -mask_atlas_region CA_ML_18_MNIA::Putamen
Remember you’re not using the TT atlas you’re using the MNI atlas to get your ROI so you have to indicate that after the
A note though: This gives you the bilateral putamen because of the :: part of the code. If you want just the right or left put the corresponding word ‘right’ or ‘left’ in between the two colons (e.g.
whereami -mask_atlas_region CA_ML_18_MNIA:left:Putamen
Overlaying this on an MNI brain looks like this is correct but please correct me if I am wrong.
The atlases with “MNIA” in their names are in the MNI_ANAT space, a shifted variant of the MNI space introduced by Eickhoff and Zilles with their SPM Anatomy Toolbox. We have other atlases for MNI space with similar names.
Am I misunderstanding that the MNIA atlases are not actually in MNI space but in some variant thereof?
I had assumed they were capable of being used with any analyses in MNI space because there are only templates included here[/url] and this link [url=https://afni.nimh.nih.gov/afni/community/board/read.php?1,156135,156168#msg-156168]here seems to allow downloads of just the Eickhoff and Zilles files as you stated above.
If so, are the other atlases anywhere specific? I have searched the site and google and nothing comes up beyond what I’ve specified.
Excuse my confusion.
MNIA atlases are not actually in MNI space but in some variant thereof. That link will get you to the “MNI” space atlases. If you look at these, they overlay the MNI atlases well, but the MNIA atlases are shifted in two directions from the MNI templates.