Scripts: Greedy extension stripping removes parts of filenames

[gdevenyi]

Greedy extension stripping such as https://github.com/ANTsX/ANTs/blob/master/Scripts/antsMultivariateTemplateConstruction2.sh#L1330

Will remove parts of files that have "." in them. Such as

Subject01.extracted.nii.gz
will be stripped to
Subject01
instead of
Subject01.extracted

sed/awk with a list of possible extensions to strip or splitting using IFS or other methods would avoid this.

[coretemp]

You can better open an issue to replace the whole script. It should not be used by people.

[gdevenyi]

Closed by #658