Hello,
I am running tbss on a group of 30 older adults tested at 2 different timepoint and have had some issues with processing the data. Currently when performing tbss_2_reg -T some of the subjects data is aligned the wrong way (the posterior portion gets aligned to the anterior of the template?).
I tried applying a fix by linearly registering all the data first but making sure to include -searchrx -180 180 -searchry -180 180 -searchrz -180 180 in the flirt command and this seems to solve the issue.
flirt -interp nearestneighbour -searchrx -180 180 -searchry -180 180 -searchrz -180 180 -in /Volumes/DANIEL/dti_FDT_FA_freesurf/${cond}.${subj}.nii.gz -ref $FSLDIR/data/standard/FMRIB58_FA_1mm.nii.gz -omat ${cond}.${subj}.flirt.mat -out ${cond}.${subj}.nii.gz
However, by doing this I am manipulating the data multiple times and would like to be able to add the -searchrx -180 180 -searchry -180 180 -searchrz -180 180 to the main tbss_2_reg source code on my computer.
I see the source code uses the following command
$FSLDIR/bin/fsl_reg $g $f ${g}_to_$f -e -FA . I am not sure if I could try and change the -FA flag to -fnirt and provide the option -searchrx -180 180 -searchry -180 180 -searchrz -180 180 inside a double quote? Or if there is a better way to do this?
Essentially I am trying to make sure when determining the optimal registration parameters in tbss_reg_2 that it searches the entire 180 degrees region.
Thank you for any help you can provide!
Daniel Callow
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