 |
 |
Hi, Unlike most tools (because it is a very old tool), the order of the options in convert_xfm cannot be altered, so you must have -omat first and then -inverse. So you should do: convert_xfm-omat $subjloud/EVfeats/$subj_EV_run$RUN_full.feat/reg/reg_output/Std2Example_func.mat -inverse $subjloud/EVfeats/$subj_EV_run$RUN_full.feat/reg/example_func2standard.mat Try this and see if it fixes the problem. All the best, Mark On 5 Dec 2012, at 23:07, Mishaela DiNino <[log in to unmask]> wrote: > 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 >