Add 3T atlas flag, remove mask from biasfield correction #406
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adapt robust rescaling, make it optional and have 2 files adapt recon-surf.sh to N4_bias_correct.py and run_fastsurfer.sh changes
… freesurfer), not ventricle intensity fix memory allocation for slurm
Change target white matter intensity in N4_bias_correct.py to 105.
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* add 3T atlas to talairach registration * add 3T atlas to pruned freesurfer installation * lower reference point of bfscaling is 1st percentile -> 3 (similar to freesurfer) * Add flags to switch to the 3T atlas for talairach registration. * Change target white matter intensity in N4_bias_correct.py to 105. * Update help text --------- Co-authored-by: Martin Reuter <[email protected]> Co-authored-by: diersk <[email protected]>
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To further address the issues with the etiv #378 , this PR adds a flag to use a 3T atlas image instead of a the default 1.5T image.
To create bias fields more similar to freesurfers bias field, the mask is deactivated.
The reference white matter intensity value for the bias field rescaling is now also 105 (aseg-method) instead of 110.