Hi folks - I would like to take overlay stats form a functional analysis on anatomical data for each of hundreds of participants, and then select 1 2d image from the anat brik to save and print as .jpg. So - I will obviously use a shell, rather than the AFNI viewer to do this.
I have looked into a number of different 3d programs that will let me select one 2D image from a 3D anatomy BRIK, but I can’t seem to find one that does what I want. For example, I will overlay stats onto the anatomical BRIK for each participant and then select 1 medial 2d slice in the saggital plane to save as a .jpg.
Is there something I’m missing? Selecting sub-bricks from 3d+time briks is easy but I couldn’t see a method for selecting a single 2D image from the 3d anat brik.
I looked at 3dcalc, 3dcopy, 3dmerge, etc…
You can SET the location based on DICOM coordinates,
SPM (LPI version), IJK indices or a voxel index. The XYZ
coordinates may be the most clear. Consider this command
from @DriveAfni:
Nowadays, I would say by far the easier way to go would be to use @chauffeur_afni, which wraps around the driving functionality in the GUI (as well as environment-variable-based features). You can make montages, control opacity and overlay thresholding, and so very much more. This program is the main workhorse behind the afni_proc.py QC HTML (APQC HTML): https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/apqc_html/apqc_ex1.html
By default, sets of axial, coronal and sagittal images are output; you can let the program evenly space slices across the full FOV or mask, or you can specify your own central coordinate and delta_slice number.
Sure thing. And indeed, sometimes asking on the Message Board is the speediest way to find some functionality.
--pt
The
National Institute of Mental Health (NIMH) is part of the National Institutes of
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