SPM Toolbox Mask Conversion

AFNI Message Board
1

Dear AFNI experts,

Hope everyone is staying safe and healthy. I am trying to use the basal forebrain mask in the SPM Anatomy Toolbox mask as a seed mask for the resting state analysis in AFNI. I downloaded the mask from the SPM webpage and converted the SPM mask to the standard MNI using @ShiftVolume -MNI_Anat_to_MNI.
I tried this earlier which showed a mask in the first attached screenshot. I was trying to redo it today and it shows a completely different mask (the second screenshot). Could you please let me know why this happened? I think the first one should be correct since the basal forebrain is a very small region. Thank you in advance for your help.

Best,
JW

NBM_mask_z=-16.jpg
NBM_mask_z=-16.jpg1544×1832 174 KB

1.jpg
1.jpg1544×1832 172 KB

2

I think you may have a different ROI each time. Look at this dataset in the MNI_ANAT space of the SPM Anatomy toolbox. What is the region called in the Anatomy toolbox. We distribute a set of atlases already in MNI space that have been transformed using this command:

@Shift_Volume -MNI_Anat_to_MNI -prefix MNI_caez_mpm_22 -dset MNIa_caez_mpm_22+tlrc

You can see all the ones distributed with your copy of AFNI with
ls ~/abin/MNI_caez_*.HEAD

I think you may be looking for one of these two regions :
whereami -atlas CA_MPM_22_MNI -show_atlas_code | grep -i bf
u:BF_(Ch_1-3):114
u:BF_(Ch_4):142