Reslicing and modifying voxel dimensions

I am doing tractography and I have my ROI’s that have been resampled. Below is my code

flirt -in SN_seeds.nii.gz -ref FA2str.nii.gz -applyisoxfm 2.0 -nosearch -out SN_seed5.nii.gz

SN_seed5.nii.gz is off center/not aligned properly. I went in using fslcpgeom to change the dimensions to the native space dimensions. But it is still not aligning to my native space brain.

Any ideas as to what I should do, I tried registration instead of resampling and I still came across the same problem

What is FA2str.nii.gz and how as it calculated?

FA2str.nii.gz comes from

flirt -in /packages/7x/fsl/6.0.2/data/standard/MNI152_T1_2mm_brain -ref fits_FA.nii.gz -out FA2str -omat FA2str.mat

fits_FA is the FA map from DTIFIT

I think I just need to replace it with the registered image from:

flirt -ref /packages/7x/fsl/6.0.2/data/standard/MNI152_T1_2mm_brain -in nodif_brain_mask (bet)
-out diff2struct_reg -omat mask2struct.mat

I just checked an the dimensions are more accurate with that overlay and then I wont have to provide the transform for the seeds space when running probtrackx

If you have your -omat FA2str.mat, then you can use that in your original flirt command. That way, the same transform used to get MNI to DWI space will be used.

flirt -in SN_seeds.nii.gz -ref fits_FA.nii.gz -applyisoxfm 2.0 -init FA2str.mat -out SN_seed5.nii.gz

Also, I dropped the -nosearch argument, as when -applyxfm or -applyisoxfm is used then there is no optimisation or search at all anyway. If you are using these as seeds, you will also want to binarize them probably. fslmaths SN_seeds5.nii.gz -bin SN_seeds5_bin.nii.gz


Thanks, as always you’ve been very helpful