Fix Timer with progress

[poquirion]

Fix #1507

[jcohenadad]

I tested poq_issue_1507_progress/32a1bf244dc13569d53ae9ec6550ebd2392151c3

The issue with the timer is fixed. Tested with:

sct_process_segmentation -i t2_seg.nii.gz -p shape

However, this issue remain:
#1507 (comment)

[poquirion]

Should be good to go now

[perone]

I added tqdm on SCT in the past for some progress bars, estimated time left, etc. I think that it can be easier to use instead of doing this manually.

[poquirion]

We can use tqdm, but we still need to add a wrapper for the logger...
tqdm/tqdm#313

I'll see how to do that best.