Hello, I am using the following to create an inverse transformation matrix from a FEAT output:
#Create inverse transformation matrix file
convert_xfm -inverse $subjloud/EVfeats/$subj_EV_run$RUN_full.feat/reg/example_func2standard.mat -omat $subjloud/EVfeats/$subj_EV_run$RUN_full.feat/reg/reg_output/Std2Example_func.mat
Then I am trying to apply that transformation matrix to an ROI I had previously created (bilateral_temporal_25.nii.gz) using the following:
flirt -in bilateral_temporal_25.nii.gz -ref /usr/local/fsl/data/standard/MNI152_T1_2mm_brain -out $subjloud/EVfeats/$subj_EV_run$RUN_full.feat/reg/reg_output/$subj_run$RUN_reg -applyxfm -init $subjloud/EVfeats/$subj_EV_run$RUN_full.feat/reg/reg_output/Std2Example_func.mat
When I look at the output ROI in fslview, it is in standard space, but the ROI is lower and farther to the right than the standard image. Is there a mistake in my command line, or should I be using a different file somewhere?
Thank you!
Mishaela
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