Hi everyone,
I have certain ROIs that are in the MNI_1mm space that I would like to bring to the subject specific DWI space to perform tractography. Using FNIRT I have registered the MNI space (A) with the subject structural space (B) as follows:
fnirt --ref=$SUBJECT_DIR/T1.nii.gz --in=$MNI_DIR/MNI152_T1_1mm.nii.gz --aff=$SUBJECT_DIR/affine.mat --cout=$SUBJECT_DIR/MNI152_FNIRTed.nii.gz
In addition I have done linear registration between the subject structural space (B) and the subject DWI space (C) as follows:
{FSLDIR}/fsl/bin/flirt -in $SUBJECT_DIR/T1.nii.gz -ref $SUBJECT_DIR/DWI_b0.nii.gz -out $SUBJECT_DIR/T1_in_DWI.nii.gz -omat $SUBJECT_DIR/T1_in_DWI.mat' -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear
I would like to combine these two transformations to create a transformation between the MNI space (A) and the subject DWI space (C).
I saw that both convert_xfm and convertwarp can be used to combine transformation but I'm faced with these issues:
i) convert_xfm requires two .mat files like so: convert_xfm -omat <outmat_AtoC> -concat <mat_BtoC> <mat_AtoB> , but for the FNIRT operation, I only get an output .nii.gz file. Is there a way to get the transformation file as a .mat file from FNIRT? How can I use convert_xfm given my previous steps?
ii) convertwarp uses two warp.nii.gz file but the transformation file from FLIRT is a .mat file. How can I use convertwarp given my previous steps?
Thanks for any help!
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