Once I perform probabilistic tractography, I wanted to visualize my tracts using suma
Following the steps on the afni link: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/SUMA/Viewer.html
I tried to run the following command
suma \ -vol o.NETS_AND_000_PAIRMAP+orig \ -vol DT_FA+orig \ -vol ../ROI_ICMAP_GMI+orig \ -gdset o.NETS_AND_000.niml.dset
I used the zeroth brick of the pairmap as indicated in the code on the website. However, I’m not getting a colour map to show up for the parimap as they do. I’m wondering if that has to do with me running probabilistic tractography?
Or does that indicate that there’s an underlying problem with my tracts because the colormap doesn’t appear in my case?
I know there is another appraoch indicated here: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/fatcat_prep/Postprocessing_IV.html
but it doesn’t allow me to visualize both the ROI’s along with the tracts (as the other method).
I wanted to add that when I ran this approach with the following code:
I got the following error message:
++ Now, start putting the files together.
++ 3dcalc: AFNI version=AFNI_18.0.22 (Feb 26 2018) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: output sub-brick 0 is all zeros!
++ Output dataset ./network6_PRE/__WDIR_connec_vis_wmc/vv_00_zero.nii
++ 3dTcat: AFNI version=AFNI_18.0.22 (Feb 26 2018) [64-bit]
*+ WARNING: Set TR of output dataset to 1.0 s
++ elapsed time = 0.1 s
I’m not quite sure why the sub-brick 0 is all zeros. Is that problematic? There are 4 ROI’s
Thanks again for your time.