We are working with some resting state acquisitions in SCT 5.0.1
So far we have managed to normalize them to the PAM50 atlas which produces a massive file of more than 1.4GB. We have been working in some approaches to try and make this file less heavy.
So far our pipeline does the following
sct_crop_image -i NormalizedResting.nii.gz -zmin 780 -zmax -1 -o NormalizedResting_crop.nii.gz fslmaths NormalizedResting_crop.nii.gz -mul 1 NormalizedResting_crop_int.nii.gz -odt int sct_resample -i NormalizedResting_crop_int.nii.gz -mm 1x1x3 -o NormalizedResting_crop_int_2_1x1x3.nii.gz
We find ourselves with a file of 23MB, which is acceptable. Nevertheless, in the last procedure, the resampling, the initial image has 120 volumes; dimensions 141,141,211; voxel size 0,5x0,5x0,5; while the output has 276 volumes; dimensions 70,70,35; voxel size 1x1x3 . Why is that happening? We would expect the output to have also 120 volumes with the corresponding dimensions and voxel size.
And if you also think of another approach to do this, feel free to share it!
Bonus: there is a typo in
sct_resample. In the
verbose section, flag 2 says
expended, should be