Dear ITK-SNAP community members,
I am trying the following
c3d commands.
The first one listed below (slightly adapted from
c3d documentation) works as expected that it produces PNG with segmentation overlaid on T1w.
c3d T1w.nrrd -stretch 2% 98% 0 255 -clip 0 255 \
tissue_labels.nrrd \
-foreach -slice z 50% -endfor \
-oli tissue_labels.txt 0.25 -type uchar -omc overlaid_approach1.png
I then tried the following adaption which conceptually feels like equivalent but is producing a PNG with only the T1w and not with the segmentation overlaid.
c3d T1w.nrrd -stretch 2% 98% 0 255 -clip 0 255 -slice z 50% \
tissue_labels.nrrd -slice z 50% \
-oli tissue_labels.txt 0.25 -type uchar -omc overlaid_approach2.png
My understanding is that the order of the images on the stack would match the order in which they appear in the command, and
-foreach -slice z 50% -endfor also preserves that order. And even though the order specification is the same in both the commands, somehow the order is being changed for the second approach but would be helpful to understand why. The main difference between the two approaches is in where the
-slice z 50% operation is performed. I uploaded the data
here. Could you kindly share your thoughts on why there would be a difference between the two approaches?
Thank you so much for your help and guidance.
Sincerely,
Nagesh