Hi,
I am using fslmaths to sum together a number of nifti labelmaps and create a summed labelmap. To do this, I have been using the command as follows:
fslmaths <input_file_1.nii> -add <input_file_2.nii> -add <input_file_3.nii> -add <input_file_4.nii> etc. <summed_output_file.nii>
The command is producing an output nifti file but is generating the following error:
WARNING:: Inconsistent orientations for individual images in pipeline!
Will use voxel-based orientation which is probably incorrect - *PLEASE CHECK*!
Additionally, when I open the output file in fsleyes, it appears to be essentially the same (in terms of size and position in MNI space) as the initial nifti input file (i.e., input_file_1) that was placed before any of the -add command. I tested this by running fslmaths again to create another summed labelmap using the same dataset but changing which input file was placed first in the command. I found that a different output file was created (once again, this was the same as the initial input file). I've attached an image (attachment 1) which shows the 2 different output files that have been created using the same dataset. I also tested whether the output nifti (intended to be a summed labelmap) actually spatially encompassed all the input files. In fact, opening the output file and then all the input files in fsleyes demonstrated that the output file was only using data from a single input file (the initial input file) (attachment 2).
Any help understanding this issue and figuring out how to properly create a summed labelmap from multiple input files would be much appreciated.
Thanks,
Gavin
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