Options when subjects fail in crop_aladin stage

[julfou81]

Inspired from subject sub-032159 in site-mountsinai-S from PRIME-DE, which fail miserably since the first step of macapype.

Here is for instance the image after the first stage:

• option 1
  -- Prepare the data with FSL-FAST:
  fast -l 8 -B sub-032159_ses-001_run-1_T1w.nii.gz
  -- Apply the reg_aladin command used in macapype to the bias corrected image:

reg_aladin -aff sub-032159_ses-001_run-1_T1w_aff.txt -flo sub-032159_ses-001_run-1_T1w_restore.nii.gz -ln 12 -lp 10 -nac -noSym -omp 1  -ref /Users/jsein/Documents/Centre_IRMf/DATA/BIDS/Covoprim/inia19-t1.nii -res sub-032159_ses-001_run-1_T1w_restore_res.nii.gz -rigOnly -smooR 1.000000

-- Apply the calculated transform to the original image

reg_resample -flo sub-032159_ses-001_run-1_T1w.nii.gz -ref /Users/jsein/Documents/Centre_IRMf/DATA/BIDS/Covoprim/inia19-t1.nii  -res test.nii.gz -trans sub-032159_ses-001_run-1_T1w_aff.tx

This is the result:

• option 2 (much faster)
  -- change the parameters of reg_aladin on the original image:

reg_aladin -aff sub-032159_ses-001_run-1_T1w_aff.txt -flo sub-032159_ses-001_run-1_T1w.nii.gz -ln 8 -lp 10 -nac -noSym -omp 1  -ref /Users/jsein/Documents/Centre_IRMf/DATA/BIDS/Covoprim/inia19-t1.nii -res sub-032159_ses-001_run-1_T1w_res.nii.gz -rigOnly -smooR 1.000000

=> same result

[julfou81]

With a little more exploration, using sites ucdavis and mount sinai-S, I had to choose between two sets of parameters for reg_aladin: (with ref inia19)

1. reg_aladin -ln 12 -lp 10 -nac -noSym -omp 1 -ref -rigOnly -smooR 1
   => works for all subjects of ucdavis and all but two subjects of mount sinai-S

2. reg_aladin -ln 5 -lp 10 -nac -noSym -omp 1 -ref -rigOnly -smooR 1
   => works for all subjects of ucdavis, mount sinai-S ( even for the two subjects of mount sinai-S that weren't working)

For INT macaques, option worked for all the one I tried, except Galileo, which needed to be cropped before and use of option 1.