Minor Error in Structural Image Registration: Could not find /tmp/fsl_[process_id]_ox_asl/tmp_asl_reg/low2high

[ellarowsthorn]

Hi everyone, I have been a user of BASIL for a while now, but have more recently been coming across an issue relating to structural image registration. Error: "could not find a supported file with prefix "/tmp/fsl_[process_id]_ox_asl/tmp_asl_reg/low2high". I believe I have found the cause.
Rest assured, this does not seem to affect any downstream processes from what I can tell, but verification of this from others is welcome!

Looking into oxford_asl.in, when BASIL runs the structural image registration there are a few potential options, such boundary-based registration (when using the --reg-init-bbr flag) or FLIRT:

if [ ! -z $reg_init_bbr ]; then
         Log "Using BBR for initial registration"
            fslmaths $regfrom -thr 0 -bin $tempdir/mask_reg_init
            extraoptions=$extraoptions" -m $tempdir/mask_reg_init --tissseg $tempdir/tissseg"
            regto=low2high_final
        else
            Log "Initial registration is FLIRT only"
            extraoptions=$extraoptions" --mainonly"
            regto=lowtohigh
        fi
# Save the registered image
 imcp $tempdir/tmp_asl_reg/$regto $tempdir/asl2struc_initial

As you may notice, the resulting file is expected to be named either "low2high_final" or "lowtohigh" respectively. However, in asl_reg.in the files are saved as "low2high" when running FLIRT, which, due to the typo, causes errors for copying the NIFTI file to asl2struc_initial. While this file usually also gets copied over to the output directory with the --qc-output flag, I don't think it is otherwise directly used by further processes.

Although I'm yet to test this myself, I believe changing this portion of the code to the below could fix the error for the FLIRT registration:

if [ ! -z $reg_init_bbr ]; then
            Log "Using BBR for initial registration"
            fslmaths $regfrom -thr 0 -bin $tempdir/mask_reg_init
            extraoptions=$extraoptions" -m $tempdir/mask_reg_init --tissseg $tempdir/tissseg"
            regto=low2high_final
        else
            Log "Initial registration is FLIRT only"
            extraoptions=$extraoptions" --mainonly"
            regto=low2high
        fi
# Save the registered image
 imcp $tempdir/tmp_asl_reg/$regto $tempdir/asl2struc_initial

TLDR: feel free to ignore so long as your structural registration otherwise worked :)