Get 2D image from 3D anatomy for overlay/jpg

AFNI Message Board
1

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…

thanks a lot, mb

2

Anyone?

3

Hi-

So, if I understand correctly, you want to make a JPG by:

  • picking one axial slice in an anatomical volume;
  • and overlaying statistical information?

You can do this by “driving” AFNI. See here for a host of things you can control from the command line:
https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.driver.html

The first example note there:


afni -com 'OPEN_WINDOW A.axialimage'       \
       -com 'SWITCH_UNDERLAY anat'           \
       -com 'SAVE_JPEG A.axialimage sss.jpg' \
       -com 'QUIT'                           \
       somedirectory

… sounds like most of what you want. You can specify a selected slice, as well, with “SET_IJK” or one of the “SET*XYZ” options.

-pt

4

Hi mb,

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:

plugout_drive -com 'SET_DICOM_XYZ A 0 20 40'              \
               -com 'SAVE_JPEG axialimage SavedAxiale.jpg'  \
               -quit

The descriptions for commands like SET_IJK are in the
file README.driver (which should be in your abin).

Does that seem reasonable?

  • rick
5

thanks Rick & ptaylor - I’m going to check it out. Can’t say I’ve “driven” AFNI, before,so I’ll take her for a ride…

6

Thanks Rick & ptaylor - The drive plugin worked well and we were able to what we wanted. thanks again, mb

Screen shot 2017-03-15 at 3.11.29 PM.jpg
Screen shot 2017-03-15 at 3.11.29 PM.jpg994×672 146 KB

7

That is great, thanks for the update!

  • rick
8

Hello,

I am struggling to print the overlay on the underlay.
Could you share your code to see what I might be doing wrong ?

My code :

afni   -noplugins -no_detach \
       -com "OPEN_WINDOW A.axialimage"  \
       -com "SWITCH_UNDERLAY anat_final.${subj}+tlrc"       \ 
       -com "SWITCH_OVERLAY stats.PW3.${subj}+tlrc 6 7"           \
       -com "SEE_OVERLAY +"  \
       -com "SET_THRESHNEW A.axialimage 0.01 p" \
       -com "SAVE_JPEG A.axialimage test1.jpg" \
       -com QUIT

Anybody would know what i'm doing wrong ?

9

Howdy-

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.

Examples are provided in this tutorial, including showing effect estimates plus statistic values as overlay and threshold volumes, respectively:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/auto_image/auto_%40chauffeur_afni.html

And for such images, please also consider the benefits of transparent thresholding, to helpfully show more data:
https://www.sciencedirect.com/science/article/pii/S1053811923002896

Please ping back if you have any further questions about making these images.

--pt

10

Wow, this is wonderful.
It is difficult through search engins to find proper script and functionalities.

Thanks for the help :D

S.

11

Sure thing. And indeed, sometimes asking on the Message Board is the speediest way to find some functionality.

--pt