Hi,
So I've aligned my two images (input and reference) and used flirt to generate a matrix, but when I try to use that matrix in applyxfm4d, it says it cannot read the mat file. (I'm aligning CYT20110701C_5_regdefault_bptfpixo_gauss1_braintest1 to CYT20110627D_default_bptfpixo_gauss1_braintest1, both of which are 4D fMRI images).
Here's the command line I use for flirt:
flirt -in /Users/yaelgrossman/Desktop/CYT20110701C.8P1/CYT20110701C_5_regdefault_bptfpixo_gauss1.nii.gz -ref /Users/yaelgrossman/Desktop/CYT20110627D.8L1/CYT20110627D_default_bptfpixo_gauss1.nii.gz -out /Users/yaelgrossman/Desktop/CYT20110701C.8P1/CYT20110701C_5_regdefault_bptfpixo_gauss1_flirt.nii.gz -omat /Users/yaelgrossman/Desktop/CYT20110701C.8P1/CYT20110701C_5_regdefault_bptfpixo_gauss1_flirt.mat
Then the applyxfm4d:
applyxfm4d /Users/yaelgrossman/Desktop/CYT20110701C.8P1/CYT20110701C_5_regdefault_bptfpixo_gauss1_braintest1.nii.gz /Users/yaelgrossman/Desktop/CYT20110627D.8L1/CYT20110627D_default_bptfpixo_gauss1_braintest1.nii.gz /Users/yaelgrossman/Desktop/CYT20110701C.8P1/CYT20110701C_5_regdefault_bptfpixo_gauss1_flirt4D_braintest1_4D.nii.gz /Users/yaelgrossman/Desktop/CYT20110701C.8P1//Users/yaelgrossman/Desktop/CYT20110701C.8P1/CYT20110701C_5_regdefault_bptfpixo_gauss1_flirt_braintest1.mat -singlematrix
This is the error:
Could not open matrix file /Users/yaelgrossman/Desktop/CYT20110701C.8P1//Users/yaelgrossman/Desktop/CYT20110701C.8P1/CYT20110701C_5_regdefault_bptfpixo_gauss1_flirt_braintest1.mat
Segmentation fault: 11
I just don't know what applyxfm4d wants from my matrix, so if anyone can help, I would be extremely grateful!
Thank you,
Yael
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